@article {pmid42153004,
year = {2026},
author = {Bogatyrenko, E and Dunkai, T and Kim, A},
title = {Core Bacterial Microbiome in Wild Sea Cucumbers (Apostichopus japonicus) from the Sea of Japan.},
journal = {Indian journal of microbiology},
volume = {66},
number = {2},
pages = {441-451},
pmid = {42153004},
issn = {0046-8991},
abstract = {UNLABELLED: The taxonomic composition of gut bacterial communities in wild Japanese sea cucumbers, Apostichopus japonicus, from coastal waters of the Russian part of the Sea of Japan was identified by high-throughput sequencing. The bacterial communities were comprised mainly of the phyla Proteobacteria (38.33-57.22%), Actinobacteriota (24.24-29.93%), Firmicutes (12.01-25.12%), and Bacteroidota (1.6-2.17%) that made up a total of 94.5% of the samples studied. As the results showed, the region and habitat have a significant effect on the bacterial structure of the gut microbiome in A. japonicus. The invertebrates from each of the water bodies under study were characterized by their unique sets of symbiotic microorganisms. However, 32 bacterial genera were found in the animals from all of the water bodies. Of these, nine bacterial genera were the dominant taxa in terms of percentage of their representation in the samples: Stappia (15.89-34.68%), Stenotrophomonas (3.45-11.44%), Bacillus (1.05-7.71%), Staphylococcus (4.64-11.76%), Rhodococcus (3.07-11.08%), Corynebacterium (2.55-7.77%), Cutibacterium (15.89-34.68%), Pseudomonas (1.2-1.7%), and Streptococcus (1.09-1.57%). The discovery of bacterial genera common across all samples indicates the existence of a core microbiome potentially essential for the host's health and functions.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-025-01493-w.},
}

@article {pmid42153502,
year = {2026},
author = {Kumar, S and Jindal, A and Mainuddin, and Rastogi, H and Kumar, A},
title = {Unraveling the Multifunctional and Translational Paradigm of Nanoparticulate Systems against Colorectal Cancer.},
journal = {ACS applied bio materials},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsabm.5c02297},
pmid = {42153502},
issn = {2576-6422},
abstract = {Colorectal cancer (CRC) is a health burden due to its high mortality rate, recurrence rate, and drug resistance. The limitations of traditional methodologies (such as radiotherapy, chemotherapy, surgery, and targeted active ingredients) include inefficient delivery to tumor tissue, systemic toxicity, drug resistance, and poor specificity. Hence, drug delivery through micro- and nanoparticulate systems offers innovations and can address these obstacles successfully. The design, functionality, and translational potential of particulate systems specifically designed for CRC treatment are reviewed in this study. Next, this review discusses various primary aspects, including the types of carriers (polymeric, solid lipid, inorganic, and hybrid nanoparticles/NP), their particulate physical attributes (size, shape, surface charge, composition), and factors affecting drug encapsulation and release kinetics that affect the basic design principles. Additionally, this review unfolds a discussion over targeting approaches, such as active ligand-mediated targeting, passive EPR-based accumulation, and stimulus-responsive systems activated by external stimuli, pH, enzymes, redox, or even the microbiome. Furthermore, conventional chemotherapeutics, phytochemicals and nutraceuticals, gene-based therapies (siRNA, miRNA), and combinatorial modalities (chemo and immunotherapy, photothermal, photodynamic) are included in the therapeutic payloads. Moreover, in vitro, in vivo, and clinical-stage nanoparticulate systems are highlighted with translational advancements. Specifically, this review emphasizes the benefits offered, including enhanced solubility, stability, targeted distribution, and multifunctionality (imaging, triggered release). In addition, primary challenges to translation, such as regulatory, scalability, reproducibility, biological processes, and long-term safety issues, are also discussed. Conclusively, innovative approaches like regulatory frameworks, microbiome-driven delivery designs, aspects of artificial intelligence/machine learning (AI/ML)-guided optimization, and stealth and biomimetic hybrid particulates can be beneficial from futuristic aspects. Suggestively, to expedite the transition from NP invention to effective CRC therapeutics, a translational roadmap is required that encourages the combination of modern materials science, computational design, and clinical validation.},
}

@article {pmid42153538,
year = {2026},
author = {Julanon, N and Unhapipatpong, C and Wongjirattikarn, R and Anutraungkool, T and Chaowattanapanit, S and Choonhakarn, C and Sawanyawisuth, K and Shantavasinkul, PC and Zouboulis, CC and Piguet, V},
title = {Role of Probiotics in Managing Acne Vulgaris: A Systematic Review and Meta-Analysis of Clinical Trials.},
journal = {Journal of cutaneous medicine and surgery},
volume = {},
number = {},
pages = {12034754261445880},
doi = {10.1177/12034754261445880},
pmid = {42153538},
issn = {1615-7109},
abstract = {BACKGROUND: Dysregulation of the skin microbiome is implicated in acne pathogenesis.

OBJECTIVE: To evaluate the efficacy of probiotics in the management of acne.

METHODS: Searches were conducted in 3 databases through June 30, 2024. Clinical trials that compared probiotics with controls and investigated their efficacy in acne were included. Primary outcomes were standardized mean differences (SMDs) for the change from baseline to posttreatment in total lesion count (TLC), noninflammatory lesion count (NILC), and inflammatory lesion count (ILC). Secondary outcomes included Global Acne Grading System (GAGS) scores, Investigator's Global Assessment, erythema, and sebum levels.

RESULTS: Thirteen studies comprising 18 study arms and 1453 participants were included. There were no significant reductions in TLC (SMD, -0.22; 95% confidence interval [CI]: -0.50 to 0.07; I[2] = 75%), NILC (SMD, -0.20; 95% CI: -0.48 to 0.08; I[2] = 72%), or ILC (SMD, -0.13; 95% CI: -0.34 to 0.09; I[2] = 52%) with probiotics compared with controls. However, oral probiotics were associated with a significant reduction in GAGS scores (SMD, -0.47; 95% CI: -0.81 to -0.13; I[2] = 67%) versus controls. Subgroup analyses indicated that this effect was most prominent in mild-to-moderate acne patients who received oral probiotics containing Lactobacillus species combined with other strains for a minimum of 12 weeks.

CONCLUSIONS: Probiotics did not demonstrate a significant reduction in acne lesion counts. However, they were associated with improvements in acne severity as measured by GAGS scores. These findings should be interpreted with caution given the heterogeneity across studies and the fluctuating natural course of acne.},
}

@article {pmid42153569,
year = {2026},
author = {Zhang, Q and Li, Y and Han, Y and Zhou, W and Li, X and Sun, J and Bai, W},
title = {Correction to "Lactiplantibacillus plantarum FEED8 Biosynthesis of Pyranoanthocyanin (Cyanidin-3-glucoside-4-vinylcatechol) Improves Oxidative Stress and Inflammation of the Gut Microbiome in Cadmium-Exposed Mice".},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c06010},
pmid = {42153569},
issn = {1520-5118},
}

@article {pmid42153643,
year = {2026},
author = {Jeilu, O and Simachew, A and Hartmann, EM and Alexandersson, E and Johansson, E},
title = {CAZyme fold architecture is conserved between disparate environments despite extreme sequence divergence.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0048526},
doi = {10.1128/msystems.00485-26},
pmid = {42153643},
issn = {2379-5077},
abstract = {Microbial carbohydrate-active enzymes (CAZymes) underpin carbon cycling across Earth's ecosystems; however, how contrasting environments shape CAZyme diversity and structural conservation remains poorly understood. Here, we applied shotgun metagenomics to compare the carbohydrate-degradation potential of two functionally prolific but physicochemically opposed ecosystems: the alkaline-saline soda lakes of the East African Rift Valley and the anaerobic ruminant gut. From 34 metagenomes (12 soda lake and 22 rumen), we recovered 371 quality-filtered metagenome-assembled genomes, of which 84% of soda lake and 52% of rumen MAGs represented novel species. Rumen communities, dominated by Bacteroidota, Fibrobacterota, and Bacillota, exhibited significantly higher taxonomic diversity and were enriched in carbohydrate catabolism and fermentation pathways. Soda lake communities, dominated by Pseudomonadota, displayed greater evolutionary divergence (lower RED scores) and were enriched in pH homeostasis, oxidative and osmotic stress, sulfur cycling, and carbon fixation pathways. To assess whether structural conservation persists despite extreme sequence divergence, we predicted three-dimensional structures for 12 representative enzymes from six glycoside hydrolase families (GH1, GH3, GH5_11, GH9, GH10, and GH28) using AlphaFold 3. All 12 structures adopted canonical GH family folds with high confidence (pTM 0.75-0.97). These results demonstrate that environmental selection drives distinct taxonomic and functional strategies for carbon processing while preserving three-dimensional CAZyme architecture, positioning soda lake and rumen metagenomes as complementary reservoirs for bioprospecting industrially relevant enzymes.IMPORTANCECarbohydrate-active enzymes, or CAZymes, are the molecular machines that microorganisms use to break down plant material and other complex sugars, and they underpin both the global carbon cycle and many industrial processes, from biofuel production to food, feed, and textile manufacturing. In this study, we compared the CAZyme repertoires of two microbial worlds that could hardly be more different: the alkaline, salty soda lakes of the East African Rift Valley, and the anaerobic stomachs of cattle, sheep, and goats. We show that although these communities are taxonomically distinct and their enzyme sequences have diverged dramatically, the three-dimensional shapes of their key carbohydrate-degrading enzymes remain remarkably well preserved. Soda lakes, in particular, hold a large pool of previously uncharacterised enzymes, identifying them as a promising, largely untapped source of robust biocatalysts for sustainable biotechnology and industrial applications.},
}

@article {pmid42153646,
year = {2026},
author = {Revel-Muroz, AZ and Sonets, IV and Chistyakov, AS and Vasiluev, PA and Surovoy, YA and Ivanova, VA and Kozlovskaya, LI and Khokhlova, OE and Fursov, MV and Fursova, NK and Ulianov, SV and Tyakht, AV},
title = {Gut Hi-C metagenomes of severe COVID-19 patients: bacteria and yeast involved in gut-lung axis.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0013926},
doi = {10.1128/msphere.00139-26},
pmid = {42153646},
issn = {2379-5042},
abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health, particularly in intensive care units, where vulnerable patients are frequently exposed to multidrug-resistant microorganisms. The human gut microbiome serves as a key reservoir for AMR genes, which can disseminate to other body sites, including the lungs, especially during severe illness. We applied Hi-C metagenomics to stool samples from 11 critically ill COVID-19 patients and analyzed microbial isolates from their lungs to investigate intra-host transmission of AMR genes. Plasmid-resolved microbial interaction networks revealed AMR gene sharing across 13 bacterial genera, primarily from Firmicutes and Proteobacteria, with evidence of plasmid-mediated transfer across phylum boundaries and between gut and lung compartments. Notably, we identified genetically identical Klebsiella pneumoniae strains colonizing both the gut and lungs of a single patient, as well as shared plasmids carrying qnrS-1 and blaCTX-M-231 resistance genes between gut Escherichia coli and lung K. pneumoniae. In addition to bacterial pathogens, Candida yeast species isolated from both niches harbored resistance genes to multiple antifungal classes, including azoles. These findings underscore the dynamic, cross-compartmental nature of AMR dissemination within the human body and highlight the importance of integrative surveillance strategies to control resistance in clinical settings.IMPORTANCEWhile COVID-19 itself caused severe illness, many deaths were ultimately due to secondary microbial infections-often worsened by antibiotic resistance. Plasmids, which shuttle resistance genes between bacterial species, are key players in their spread, yet their roles in transmission, especially across body sites such as the gut and lungs, are to be elucidated. The use of Hi-C metagenomics allowed us to map bacterium-plasmid links in the guts of severe COVID-19 patients and reconstruct high-quality genomes of opportunistic fungi. Comparing these with lung-derived isolate genomes, we gained insight into possible intra-host dissemination routes of resistance genes. Preparing for future pandemics will require not only rapid pathogen detection but also tools to monitor microbiome health and resistance dynamics, and understanding how treatments and microbial imbalances shape infection risks.},
}

@article {pmid42153658,
year = {2026},
author = {Chen, X and Chen, GG and Gong, Z and Zhu, H and Liang, Z and Chan, JYK and Tong, MCF and Chen, Z and Chang, WT},
title = {The middle ear-nasopharyngeal microbiome axis associated with obstructive Eustachian tube dysfunction in chronic otitis media.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0000726},
doi = {10.1128/msystems.00007-26},
pmid = {42153658},
issn = {2379-5077},
abstract = {Obstructive Eustachian tube dysfunction (ETD) commonly complicates chronic otitis media (COM), yet microbial factors at the Eustachian tube (ET) openings remain poorly understood. In this prospective cohort study, we characterized the microbiota at both the middle ear (ME) and nasopharyngeal (NP) ET openings in COM patients undergoing ear surgery and examined associations with obstructive ETD over one year of follow-up. Using 16S rRNA gene sequencing and functional inference, we profiled microbial communities from the ME-side ET opening and the torus tubarius on both surgical-side and contralateral nasopharynx. Among 37 patients (18 with ETD, 19 without), ME and NP microbiota differed significantly in composition. Ears with ETD showed increased ME microbial diversity and enrichment of Neobacillus, Agrobacterium, and Sphingomonas. Paired NP-ME analyses indicated an altered NP-ME microbial relationship in ETD, with Neobacillus showing a nasopharyngeal source signal. Functional prediction revealed increased porphyrin metabolism and decreased pyruvate metabolism in ME microbiota with ETD, suggesting a shift toward biofilm formation and altered redox states. Anaerococcus was increased in the nasopharynx of patients with bilateral COM. These findings identify distinct microbial and metabolic features of COM with obstructive ETD, supporting a role for nasopharyngeal-microbial influence on ME pathology.IMPORTANCEChronic otitis media (COM) is a common and often persistent ear disease, especially when complicated by Eustachian tube dysfunction (ETD). By profiling microbiota at both Eustachian tube openings, this study links upper-airway microbial ecology with middle-ear microbial states in COM and helps clarify where clinically relevant signals may arise along the Eustachian tube pathway. The paired nasopharyngeal-middle ear design revealed that nasopharyngeal microbes may be linked to middle-ear community shifts in COM with obstructive ETD, consistent with a potential upper airway contribution to the middle-ear microbiota, generating testable hypotheses about microbial exchange and persistence. These findings highlight the upper airway microbiome as a potential target for developing new preventive and therapeutic strategies in COM.},
}

@article {pmid42153706,
year = {2026},
author = {Borren, NZ and Paulides, E and Klaassen, MAY and Alm, E and Xavier, RJ and Janneke van der Woude, C and Ananthakrishnan, AN},
title = {Microbiome-Directed Therapy for Fatigue in Quiescent Inflammatory Bowel Disease: A Randomized Placebo-Controlled Trial of Multi-Strain Probiotic Supplementation.},
journal = {The American journal of gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.14309/ajg.0000000000004056},
pmid = {42153706},
issn = {1572-0241},
abstract = {INTRODUCTION: Fatigue is a challenging symptom for patients with inflammatory bowel diseases (IBD). Emerging evidence links alterations in the gut microbiome with fatigue in IBD, highlighting the potential of microbiome-targeted treatments. Our aim was to evaluate the clinical efficacy and biological effects of a multi-strain probiotic supplementation on fatigue in patients with quiescent IBD.

METHODS: This multi-center, placebo-controlled, randomized controlled trial included patients with quiescent IBD, defined as being in clinical remission and a colonoscopy within 1 year which demonstrated no active disease, and with significant fatigue (FACIT-F score < 43). Patients were randomized to receive either probiotics (Ecologic® BARRIER, containing 9 different bacterial strains) or placebo for 12 weeks. Gut microbiome and serum metabolome were analyzed at baseline and at the end of the study.

RESULTS: Our study enrolled 100 patients (52 Crohn's disease (CD), 44 ulcerative colitis (UC), 4 IBD-unspecified) with quiescent IBD and with a mean age of 41 years; 61% were women. After 12 weeks, 29.4% of the probiotic group and 40.0% of the placebo group met criteria for no fatigue (p=0.34). However, all participants reported an improvement in fatigue (p<0.001) with the most striking change noted at 4 weeks in both groups. Probiotic treatment led to beneficial shifts in gut microbiome and serum metabolome composition, particularly an increase in Bifidobacterium animalis after 12 weeks.

DISCUSSION: While 12 weeks of probiotic administration was not associated with relief of fatigue in patients with quiescent IBD, we observed beneficial alterations in the gut microbiome and serum metabolome. ClincialTrials.gov number, NCT03266484.},
}

@article {pmid42153723,
year = {2026},
author = {O'Sullivan, B and Herbst, KW and Hogan, AH and Maltz-Matyschsyk, M and Radolf, JD and Lawrence, D and Lynes, MA and Salazar, JC and Graf, J and , },
title = {Comparison of a long-read amplicon sequencing approach to short-read amplicons for microbiome analysis.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0277625},
doi = {10.1128/spectrum.02776-25},
pmid = {42153723},
issn = {2165-0497},
abstract = {UNLABELLED: Most microbiome studies to date rely on sequencing short amplicons of the 16S rRNA gene on Illumina's platforms. Because of the short read length, sequences often can be identified reliably only to the family or genus levels. Long-read sequencing with whole-length 16S rRNA sequencing can improve taxonomic resolution but often only to the species level. StrainID is an alternative approach that amplifies a large segment of the ribosomal operon, including the entire 16S rRNA gene, internal transcribed spacer, and a portion of the 23S rRNA gene. This longer amplicon is designed to allow ribotype-level classification. Although studies have demonstrated the utility of StrainID for several sample types, a direct comparison of StrainID to alternative approaches has not been done for saliva. Here, we compared the performance of StrainID to short-read amplicons with saliva samples as well as a synthetic mock DNA community. Short reads were amplified with primer pairs targeting the V1-V3 region of the 16S rRNA gene and were classified with several different taxonomic databases. We found that StrainID outperformed short reads not only in identifying amplicon sequence variants to the species level but also in demonstrating a key benefit with phylogenetic-based beta-diversity tests. Our results further build on establishing StrainID as a powerful method and specifically for its use with saliva samples.

IMPORTANCE: The interpretation of microbiome composition studies is highly dependent on the methodologies chosen during experimental design, which affects factors such as resolution, throughput, cost, and accuracy. StrainID is an approach that can improve resolution while maintaining high-throughput and similar costs to short-read sequencing. The salivary microbiome represents a diverse community of microbes with links to a variety of health conditions and disease states. Closely related strains of bacteria can have drastically different effects on their host. Establishing StrainID as a valid approach for studying the salivary microbiome opens avenues for research that improve upon alternative methods by increasing sensitivity and accuracy compared to traditional short-read approaches.},
}

@article {pmid42153897,
year = {2026},
author = {Jain, M and Babu, R and Jain, A},
title = {Phosphate binders and the gut microbiota in chronic kidney disease: mechanisms, mixed evidence, and clinical considerations.},
journal = {Journal of nephrology},
volume = {},
number = {},
pages = {},
doi = {10.1093/joneph/aajag023},
pmid = {42153897},
issn = {1724-6059},
abstract = {Chronic kidney disease (CKD) disrupts the gut microbiome through dietary restrictions, uraemia, and polypharmacy, including phosphate binders. This dysbiosis contributes to systemic inflammation, accumulation of uremic toxins, and reduced short-chain fatty acid (SCFA)-producing bacteria. Hyperphosphatemia, a key CKD complication, typically emerges in advanced stages. This review examines the impact of phosphate binders on gut microbiota and explores emerging biological therapies. Phosphate binders are standard treatment for hyperphosphatemia but may influence gut microbiota by altering luminal pH, intestinal transit, and availability of metabolites such as SCFAs and vitamin K. These changes can impair gut barrier integrity and promote inflammation. Evidence on their microbiome effects is mixed: some studies show minimal compositional changes with calcium acetate or sucroferric oxyhydroxide, while others report individual variability and subtle taxon-specific shifts, particularly with iron-based binders. Even when compositional changes are limited, certain binders may modulate uremic toxin levels. Given the limitations of conventional therapies, biological approaches such as probiotics, synbiotics, and phosphate-accumulating organisms (PAOs) are gaining interest. These strategies may reduce intestinal phosphate availability by lowering pH, enhancing calcium-phosphate binding, and promoting microbial phosphate uptake and storage, while supporting gut barrier function. Overall, current evidence remains heterogeneous and limited by small cohorts and preclinical designs. Although microbiota-targeted therapies show mechanistic promise, robust clinical trials are needed before they can be recommended beyond adjunctive use.},
}

@article {pmid42153961,
year = {2026},
author = {Zhu, B and Chen, S and Diao, Y and Wang, W and Huang, Y and Liang, L and Lu, X and Han, R and Guo, M and Li, Z and Wang, S and Li, H and Liu, C and Zhou, J and Xiong, D and Li, X and Ning, Y and Shi, X and Wu, F and Wu, K},
title = {Dissecting the Ecological Structure of Health and Disease in the Global Gut Microbiome.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e17087},
doi = {10.1002/advs.202517087},
pmid = {42153961},
issn = {2198-3844},
support = {2023YFC2414500//National Key Research and Development Program of China/ ; 2023YFC2414504//National Key Research and Development Program of China/ ; 2025YFC3410000//National Key Research and Development Program of China/ ; 2025YFC3410005//National Key Research and Development Program of China/ ; 82271953//National Natural Science Foundation of China/ ; 82301688//National Natural Science Foundation of China/ ; 2023B0303020001//Key Research and Development Program of Guangdong/ ; 2023B0303010003//Key Research and Development Program of Guangdong/ ; 2024A1515013058//Natural Science Foundation of Guangdong Province/ ; 2025A1515010507//Natural Science Foundation of Guangdong Province/ ; 2023A1515011383//Natural Science Foundation of Guangdong Province/ ; 2019B121203008-KJ-2024-040/KJ-2024-041//Guangdong Key Laboratory of Battery Safety at Guangzhou Institute of Energy Testing/ ; 2025A03J3357//Science and Technology Program of Guangzhou/ ; ZDYN-2024-A-121//Clinical Collaboration Project on Integrated Traditional Chinese and Western Medicine for Major and Difficult Diseases/ ; 2024SRP200//Research Capacity Improvement Project of Guangzhou Medical University/ ; GCAAL2022001//Guangzhou Key Clinical Specialty (Clinical Medical Research Institute), the Announcement and Leading Science and Technical Foundation of Guangzhou Civil Affairs/ ; 2023B04J0106//Guangzhou Planned Project of Science and Technology/ ; 2025B04J0011//Guangzhou Planned Project of Science and Technology/ ; },
abstract = {The gut microbiota plays a crucial role in human health, but its coordinated ecological dynamics remain largely unclear. We present Wiredancer, a novel scalable framework based on similarity-constrained non-negative matrix factorization (NMF), which extracts continuous and overlapping microbial ecological factors (MEFs). By integrating 20,178 metagenomes spanning 36 countries and over 50 disease states, Wiredancer identified three robust and interpretable MEFs delineating the health-disease continuum. MEF1, the dysbiotic factor dominated by Bacteroides uniformis, was elevated in disease populations; MEF2, the protective factor characterized by Prevotella copri, was reduced compared with the healthy group; and MEF3, the intermediate factor represented by Bifidobacterium adolescentis, reflected a mixed ecological configuration between MEF1 and MEF2. MEFs exhibited high reproducibility across individuals and longitudinal cohorts, but showed significantly increased variability in disease, consistent with the Anna Karenina principle and highlighting disrupted ecological stability. These findings were validated in the largest Chinese metagenomic cohort of major psychiatric disorders, where MEFs were associated with clinical symptoms, peripheral biomarkers, and disease subtypes, and remained essentially stable under short-term treatment. Together, Wiredancer provides a generalizable strategy to define microbiome states and decode ecological transitions, offering new opportunities for precision diagnostics and stratified medicine in complex disorders.},
}

@article {pmid42154316,
year = {2026},
author = {Ulrich, JF and Redlich, SB and Mohr, A and Vollmers, J and Petersen, J and Wichard, T},
title = {Marine Rhodobacterales as Drivers of Ulva Growth: From Macroalgal-Bacterial Interactions to Bioactive Factor Enrichment.},
journal = {Journal of chemical ecology},
volume = {52},
number = {3},
pages = {},
pmid = {42154316},
issn = {1573-1561},
mesh = {*Ulva/growth & development/microbiology ; *Seaweed/growth & development/microbiology ; },
abstract = {Marine bacteria significantly influence the development and productivity of algal communities. The green seaweed Ulva (Chlorophyta) relies on bacteria that secrete algal growth and morphogenesis-promoting factors (AGMPF). In a reductionist model system of Ulva compressa (cultivar U. mutabilis), the diverse microbiome can be substituted by two key bacteria, Roseovarius sp. MS2 and Maribacter sp. MS6, both of which release AGMPFs, thereby inducing cell division and cell differentiation. Our study examined various algal growth-promoting substances produced by marine Rhodobacterales (Alphaproteobacteria). The exploration survey indicated that 74 of the 97 examined strains demonstrated growth-promoting, cytokine-like action. These findings underscore the extensive impact of marine Rhodobacterales on Ulva growth. Bioactive fractions containing AGMPF activity were enriched from the culture supernatant of Roseovarius sp. strain MS2. Bioactive raw extracts were obtained through bioassay-guided fractionation and semi-preparative high-performance liquid chromatography; cell division-promoting properties were observed, but did not reach the activity level of the harvested supernatant. This study provides new insights that underscore the importance of bacterial-macroalgal interactions for marine ecosystems. Replacing bacteria with AGMPFs, including thallusin, enables the complete thallus formation of axenic Ulva cultures, facilitating various applications in biotechnology and aquaculture.},
}

*Ulva/growth & development/microbiology
*Seaweed/growth & development/microbiology

@article {pmid42154337,
year = {2026},
author = {Sain, M and Rani, S and Singh, SP and Pothal, P and Yadav, S and Suttee, A and Kumar, A and Kumar, S and Ranawat, P and Singh, G and Barnwal, RP},
title = {The Influence of Gut Microbiome on Alpha-Synuclein Aggregation: Implications for Parkinson's Disease Pathogenesis.},
journal = {Molecular neurobiology},
volume = {63},
number = {1},
pages = {},
pmid = {42154337},
issn = {1559-1182},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Parkinson Disease/metabolism/pathology/microbiology ; *alpha-Synuclein/metabolism ; Animals ; Dysbiosis ; *Protein Aggregates ; },
abstract = {Parkinson's disease (PD) is a progressive neurodegenerative disorder traditionally characterized by dopaminergic neuronal loss in the substantia nigra and the accumulation of misfolded α-synuclein (α-syn) aggregates. While genetic susceptibility and environmental exposures are well-recognized contributors to PD, growing evidence indicates that disease initiation and progression may also involve peripheral mechanisms originating in the gastrointestinal (GI) tract. Early non-motor symptoms such as constipation, along with the presence of α-syn pathology in the enteric nervous system, have led to increasing interest in the gut-brain axis as a critical modulator of PD pathogenesis. Recent literatures reveal that gut microbiota dysbiosis can influence neurodegeneration through immune activation, intestinal barrier dysfunction, and altered production of microbial metabolites, including short-chain fatty acids, bile acids, lipopolysaccharides, and tryptophan-derived compounds. However, the precise molecular mechanisms by which these microbial factors modulate α-syn aggregation, propagation, and clearance remain incompletely understood. In this article, we review current clinical and experimental literature linking gut microbiota alterations to α-syn pathology, with particular emphasis on inflammatory signaling, microbial metabolites, and impaired proteostatic pathways that promote α-syn misfolding. We further integrate emerging concepts of "body-first" and "brain-first" PD subtypes and discuss proposed routes of α-syn transmission from the enteric to the central nervous system, including vagal, hematogenous, and immune-mediated pathways. By highlighting underexplored mechanistic connections between gut dysbiosis and α-syn biology, this review underscores the potential of microbiome-targeted strategies for early diagnosis and disease modification. A deeper understanding of gut-brain communication may ultimately enable personalized therapeutic approaches and reshape current paradigms of PD pathogenesis.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Parkinson Disease/metabolism/pathology/microbiology
*alpha-Synuclein/metabolism
Animals
Dysbiosis
*Protein Aggregates

@article {pmid42154370,
year = {2026},
author = {Benekos, K and Katsanos, A and Laspas, P and Panos, GD and Vagiakis, I and Fousekis, FS and Luca, R and Zhou, B and Kostoulas, C and Georgiou, I and Katsanos, KH and Skondra, D and Konstas, AG},
title = {An Update and Overview of the Ocular and Extraocular Microbiome and Its Impact on Ophthalmic Care.},
journal = {Advances in therapy},
volume = {},
number = {},
pages = {},
pmid = {42154370},
issn = {1865-8652},
abstract = {The microbiome has been described as the last human "organ" and is currently the topic of great research interest worldwide. The application of culture-independent methods, like 16S ribosomal next-generation sequencing, has offered researchers the opportunity to identify bacterial populations that were impossible to detect previously using conventional culture methods. Further standardization of these new approaches to characterizing the microbiome is desirable. The present review discusses the mounting evidence suggesting that alterations in the microbiome and microbial metabolites, such as short-chain fatty acids in the gut, mouth, and ocular surface, may play a key role in the pathogenesis of ocular pathologies such as ocular surface disease, glaucoma, uveitis, age-related macular degeneration, and diabetic retinopathy. Clarifying the probable role of the microbiome in ocular diseases would not only offer valuable insights into pathogenesis but could also enable the development of novel therapeutic approaches. As yet, microbial-based therapeutic applications in ophthalmology are limited. Nevertheless, recently emerging strategies utilizing probiotics and prebiotics, or even fecal transplantation to regulate microbiome composition, offer promising research avenues for developing future innovative therapies for ocular diseases. Further studies employing standardized methodological protocols are needed to ensure the reproducibility of results and to eventually unlock the precise links between the microbiome and the eye.},
}

@article {pmid42154646,
year = {2026},
author = {Alciati, A and Cracò, F and Burgio, A and Pezzano, A and Atzeni, F},
title = {Fibromyalgia and metabolic syndrome: prevalence, potential shared pathophysiological mechanisms and non-pharmacological treatment strategies.},
journal = {Clinical and experimental rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.55563/clinexprheumatol/y4a7s4},
pmid = {42154646},
issn = {0392-856X},
abstract = {Fibromyalgia (FM) is a chronic pain syndrome defined by widespread musculoskeletal pain, fatigue and sleep disturbances, frequently accompanied by metabolic disturbances. Among these, metabolic syndrome (MetS), a cluster of abdominal obesity, hypertension, dyslipidaemia and impaired glucose regulation, stands out because of its strong association with cardiovascular disease and type 2 diabetes. Recent studies suggest that MetS and its individual components, particularly obesity, are highly prevalent in FM populations, raising important clinical and pathophysiological questions.Both FM and MetS are associated with chronic low-grade inflammation, autonomic nervous system dysfunction, and dysregulation of the hypothalamic-pituitary-adrenal (HPA) axis. Moreover, environmental factors, particularly early-life stress, may increase vulnerability by triggering persistent neuroendocrine and immune alterations. These overlapping pathways not only predispose to comorbidity but also contribute to increased symptom burden and therapeutic complexity. Systematic screening for MetS in patients with FM may improve cardiovascular risk stratification and inform more comprehensive treatment strategies. This narrative review summarises current evidence on the comorbidity of FM with MetS and its individual components, highlighting their shared pathophysiology. It also explores the therapeutic potential of non-pharmacological strategies, including structured exercise, dietary interventions, and microbiome-targeted approaches, that address common underlying mechanisms and hold promise for improving long-term outcomes.},
}

@article {pmid42155002,
year = {2026},
author = {Meng, X and Wu, X and Sun, H and Cong, J and Gu, Y},
title = {Maternal-Infant Gut Microbiota Transmission and the Early Origins of Metabolic Liver Diseases: Mechanisms and Interventional Opportunities.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag074},
pmid = {42155002},
issn = {1753-4887},
support = {42307182//National Natural Science Foundation of China/ ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease is associated with a growing global health burden with increasing prevalence in both adult and pediatric populations. Emerging evidence suggests that the origins of steatotic liver disease may trace back to early life, with the gut microbiota serving as a critical mediator in this developmental programming. This review synthesizes current knowledge on maternal-infant gut microbiota transmission and its role in shaping long-term liver health through the gut-liver axis. We examined key maternal factors, including delivery mode, feeding of breast milk, diet, metabolic status, and antibiotic exposure, that profoundly influence infant microbiota assembly. The critical window of microbiota establishment during the first 1000 days shapes intestinal barrier function, immune development, and metabolic pathways that persist into adulthood. Mechanistically, early dysbiosis contributes to metabolic dysfunction-associated steatotic liver disease pathogenesis through multiple interconnected pathways, including compromised intestinal barrier integrity facilitating endotoxemia, altered short-chain fatty acid production affecting energy metabolism and inflammation, disturbed bile acid signaling disrupting metabolic homeostasis, and epigenetic modifications potentially shaping long-term susceptibility. We critically evaluated emerging microbiota-targeted interventional strategies during pregnancy and infancy, including probiotics, human milk oligosaccharide supplementation, and synbiotic approaches, highlighting their potential for disease prevention. This review uniquely integrates concepts of developmental origins with detailed gut-liver axis mechanisms, emphasizing the maternal-infant microbial continuum as an underexplored but promising target for preventing metabolic liver disease. While significant research challenges remain, particularly in establishing causality and developing personalized interventions, modulation of the early gut microbiome offers an innovative preventive strategy against the rising tide of metabolic dysfunction-associated steatotic liver disease, potentially disrupting the intergenerational cycle of metabolic disease.},
}

@article {pmid42155039,
year = {2026},
author = {Wang, L and Wang, Q and Wolfe, TM and Pinkham, NV and Erickson, R and Yoshinaga, M and Mcdermott, TR and Walk, ST},
title = {Technical and biological factors driving inter-individual body burden of arsenic species in murine models of human arsenic exposure.},
journal = {Toxicological sciences : an official journal of the Society of Toxicology},
volume = {},
number = {},
pages = {},
doi = {10.1093/toxsci/kfag055},
pmid = {42155039},
issn = {1096-0929},
abstract = {Arsenic is one of the most important environmental toxicants, requiring advanced analytical techniques to resolve individual species. There is little consensus on arsenic speciation methodology for in vivo studies. The objectives of this study were to generate a robust framework for arsenic speciation in murine models of human exposure and evaluate factors influencing the levels of arsenobetaine, inorganic arsenite, dimethylarsinate, monomethylarsonate, and inorganic arsenate resolved by HPLC-ICPMS. Enzyme-assisted digestion by papain vs. pepsin and maceration by bead beating vs. mechanical homogenization were evaluated using chemical standard spiking experiments. Dose-controlled mouse exposures to inorganic arsenite were conducted and species detected in urine and bladder tissue were compared. Species in stool, liver, and bladder were compared between groups of mice eating a standard vs. purified diet; fasted vs. unfasted mice; and conventional vs. germ-free mice. Finally, between-lab differences in HPLC-ICPMS instrumentation/quantification procedures were evaluated. These comparisons led to several important conclusions including: Significant conversion of inorganic arsenate to arsenite by papain, significant inorganic arsenate background in bead-beating lysing matrix, significant arsenobetaine in mice eating standard but not purified chow, significant correlation between species detected in urine and bladder, significant correlation of results between laboratories that differed in absolute quantification, and large inter-individual variability between mice of the same treatment group. Finally, diet type and the presence of a microbiome had the largest effect on arsenic species levels. Our results provide a benchmark for evaluating arsenic species in murine models, including adequate sample sizes for powering studies to avoid erroneous conclusions.},
}

@article {pmid42155496,
year = {2026},
author = {Hull, RC and Liu, Y and Cao, Z and Xuan, KTL and de Lima Headley, DA and Richardson, H and Hennayake, C and Lind, H and McIntosh, E and Pollock, J and Hughes, C and Viligorska, K and Choi, H and Gao, Y and Chotirmall, SH and Shoemark, A and Robertson, K and Burgel, PR and Vendrell, M and Xu, X and Qu, JM and Song, Y and Guan, WJ and Chen, R and Singh, S and Talwar, D and Mohan, BVM and Tripathi, SK and Swarnakar, R and Trivedi, S and Goeminne, PC and Shteinberg, M and De Soyza, A and Altenburg, J and Haworth, CS and Sibila, O and Polverino, E and Loebinger, MR and Ringshausen, FC and Mertsch, P and Lorent, N and Dimakou, K and Mendez, R and Mclaughlin, AM and Borrill, Z and Lord, R and Finch, S and Blasi, F and Burr, L and Crisafulli, M and Keating, R and Middleton, PG and Long, MB and Aliberti, S and Morgan, L and Dhar, R and Chalmers, JD and Xu, JF and , },
title = {Comorbid diabetes disease severity and microbial changes in patients with bronchiectasis: a combined analysis of data from the EMBARC, EMBARC-India, Australian, and BE-China registries.},
journal = {The Lancet. Respiratory medicine},
volume = {},
number = {},
pages = {},
doi = {10.1016/S2213-2600(26)00057-3},
pmid = {42155496},
issn = {2213-2619},
abstract = {BACKGROUND: Bronchiectasis and diabetes commonly coexist and are associated with immune dysfunction and increased susceptibility to infection. Although diabetes is associated with worse prognosis in cystic fibrosis-related bronchiectasis, data are scarce for its impact on non-cystic fibrosis bronchiectasis. This study aimed to characterise the impact of diabetes on clinical outcomes and microbial and inflammatory profiles in patients with bronchiectasis.

METHODS: This analysis comprised data from the European Bronchiectasis Registry (EMBARC), Respiratory Research Network of India (EMBARC-India), Chinese Bronchiectasis Registry (BE-China), and Australian Bronchiectasis Registry (ABR); 30 263 patients with CT-confirmed bronchiectasis in 33 countries were included in the analysis: 16 963 from EMBARC (Jan 12, 2015, to April 12, 2022), 2361 from EMBARC-India plus additional Asian countries (June 1, 2015, to Sept 1, 2017), 10 324 from BE-China (Jan 10, 2020, to March 31, 2024), and 615 from the ABR (March 7, 2016, to Sept 11, 2018). Clinical data were compared between patients with and without diabetes. Long-term outcome data were available in EMBARC and EMBARC-India. Microbiome and inflammatory profiles were characterised in a sub-cohort of EMBARC patients by sputum 16S rRNA sequencing (n=433) and serum Olink (n=479).

FINDINGS: 2487 (8·2%) of 30 263 patients with bronchiectasis had diabetes. Patients with diabetes had a higher prevalence of comorbidities than those without diabetes, including cardiovascular disorders (53·5% vs 21·8%, p<0·0001), asthma (27·5% vs 21·0%, p<0·0001), and chronic obstructive pulmonary disease (34·3% vs 19·0%, p<0·0001). Patients with diabetes had more severe disease than those without diabetes, with higher Bronchiectasis Severity Index scores (8 [IQR 5-12] vs 7 [4-10], p<0·0001) and UK Medical Research Council (MRC) dyspnoea scores (p<0·0001) and more hospital admissions in the previous year (p<0·0001). After adjustment for confounders, outcomes were significantly worse in patients with diabetes than in those without diabetes, including more frequent exacerbations (incidence rate ratio [IRR] 1·18 [95% CI 1·09-1·28], p<0·0001), hospital admissions (IRR 1·57 [1·40-1·76], p<0·0001), and higher 5-year mortality (hazard ratio 1·80 [1·53-2·12], p<0·0001). The sputum microbiome was significantly altered in patients with diabetes compared to those without diabetes, with increased isolation of Enterobacteriaceae (p<0·0001), Moraxella catarrhalis (p=0·0035), and Haemophilus influenzae (p=0·046). In serum, Gal-4 and GDF-15, established biomarkers of disease severity and cardiovascular risk in diabetes, were significantly increased in patients with diabetes (Gal-4, p<0·0001; GDF-15, p=0·0019).

INTERPRETATION: Patients with diabetes and bronchiectasis are a high-risk population with more severe disease, worse outcomes, increased comorbidities, and increased risk of infections compared with patients without diabetes. These findings support inclusion of diabetes as a risk factor in individualised risk assessments for bronchiectasis.

FUNDING: European Respiratory Society, Armata, AstraZeneca, Boehringer Ingelheim, Chiesi, CSL Behring, GSK, Grifols, Insmed, Janssen, Lifearc, Roche, Verona Pharma, Zambon, National Natural Science Foundation of China, Innovation Program of the Shanghai Municipal Education Commission, Program of the Shanghai Municipal Science and Technology Commission, Program of the Shanghai Shenkang Development Center, EU/European Federation of Pharmaceutical Industries and Associations, Innovative Medicines Initiative, and Inhaled Antibiotics in Bronchiectasis and Cystic Fibrosis Consortium.},
}

@article {pmid42155536,
year = {2026},
author = {Shahvali, N and Adibi, M and Mohebi, A and Mousavianfard, SR and Salehi, M and Zamani, S and Sharifianjazi, F and Chegini, L and Bastami, F},
title = {Mesenchymal stem cell therapy for treatment of medication related osteonecrosis of the jaw (MRONJ): A systematic review.},
journal = {Tissue & cell},
volume = {102},
number = {},
pages = {103489},
doi = {10.1016/j.tice.2026.103489},
pmid = {42155536},
issn = {1532-3072},
abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw (MRONJ) is a significant adverse effect associated with antiresorptive and antiangiogenic therapies. Therapies utilizing mesenchymal stem cells (MSCs) represent a promising regenerative strategy; however, conventional management methods have shown limited effectiveness. This systematic review aimed to evaluate the effectiveness of MSC-based interventions in preventing and treating MRONJ.

METHOD: A comprehensive literature search was conducted using PubMed, Scopus, and Web of Science to identify studies published from 2011 to 2024. Studies examining MSCs therapy in the context of MRONJ were incorporated according to predefined inclusion and exclusion criteria.

RESULTS: Seventeen studies (6 clinical, 11 preclinical) met inclusion criteria. Preclinical models demonstrated that MSCs enhance angiogenesis and bone regeneration, providing mechanistic support for human application. Clinically, 80-90% of patients achieved complete mucosal healing with radiographic evidence of bone regeneration. However, due to species differences in oral microbiome and immunity, animal findings require confirmation in human trials.

CONCLUSION: This review integrates human clinical data with mechanistic insights from preclinical studies. Human evidence shows promising mucosal and bone regeneration, while animal studies elucidate underlying mechanisms-particularly angiogenesis and immunomodulation. Given that animal models cannot replicate the human oral immune environment, these findings should be interpreted as hypothesis-generating. MSC therapy represents a biologically sound but experimental strategy, warranting confirmation through randomized controlled trials.},
}

@article {pmid42155708,
year = {2026},
author = {Biber, P and Muhammad, AR and Hartinger, T and Reisinger, N and Gressley, T and Zebeli, Q and Castillo-Lopez, E},
title = {Elucidating the separate and synergistic impacts of ruminal and hindgut acidosis on fermentation and microbiome of dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-27887},
pmid = {42155708},
issn = {1525-3198},
abstract = {The aim of this study was to evaluate the short-term impacts of both subacute ruminal acidosis (SARA) and hindgut acidosis (HGA) on the ruminal and fecal fermentation and microbiome of dairy cows. The study was conducted as a change-over design using 9 rumen-cannulated Holstein cows (724 ± 79 kg body weight and 198 ± 74 d in milk). The SARA was induced by feeding a diet containing 65% concentrate (DM basis), and HGA was induced through daily abomasal infusion of 3 kg of starch (1:1 corn to wheat weight ratio). The evaluated treatments were 1) a control diet containing 40% concentrate (CON), 2) CON+HGA, 3) a diet containing 65% concentrate (SARA), and 4) SARA+HGA. Ruminal pH was measured every 15 min, and the fecal pH was measured 3 times per day (0, 6 and 12 h relative to feeding). Ruminal and fecal samples were collected in the morning before first feeding and were analyzed for microbiome through 16S rRNA gene amplicon sequencing. Additionally, rumen and fecal samples were taken at 0, 6 and 12 h relative to feeding and were analyzed for volatile fatty acids (VFA) and lactate to evaluate postprandial effects of treatments. Results showed that changing from CON to SARA lowered ruminal pH and increased ruminal propionate, without affecting fecal VFA profile or pH. Compared with CON, SARA shifted the ruminal microbiome, decreased α diversity in the rumen and feces, and increased abundance of several taxa such as Succinivibrionaceae UCG-001 (OTU 2994), Lachnospiraceae (OTU 3043), and Acetitomaculum (OTU 80). The HGA decreased fecal pH, increased total fecal VFA at 12 h post-feeding, and increased fecal lactate and butyrate at the expense of acetate and propionate. In addition, HGA shifted the fecal microbiome and increased butyrate producing bacteria such as Lachnospiraceae (OTU 18), Blautia (OTU 508), Acetitomaculum (OTU 622), resulting in positive correlations between fecal butyrate and abundance of these taxa; however, family Ruminococcaceae (OTU 1580), and Christensenellaceae (OTU 550) decreased in feces and correlated negatively with fecal butyrate. Moreover, results showed that SARA in combination with HGA aggravates shifts of the fecal microbiome as revealed by further reductions of microbial α diversity indices and families Ruminococcaceae (OTU 1580) and Christensenellaceae (OTU 550) in cows receiving the SARA diet and abomasal starch infusion. Overall, new findings from this study reveal not only separate effects of SARA and HGA on ruminal and fecal fermentation but also show additive negative impacts particularly on fecal microbial diversity and increase in fecal butyrate and lactate. Such alterations in microbial profile increase the risk of creating niches for pathogens proliferation and fecal shedding.},
}

@article {pmid42155725,
year = {2026},
author = {Intze, E and Schaubeck, M and Arendt, BM and Fleddermann, M and Beyer, K and Clavel, T and Lagkouvardos, I and Hitch, TCA and , },
title = {Mixed feeding and mode of birth modulate the effects of a hydrolyzed synbiotic formula on the gut microbiome in infants at risk of atopic disease.},
journal = {Clinical nutrition ESPEN},
volume = {},
number = {},
pages = {103338},
doi = {10.1016/j.clnesp.2026.103338},
pmid = {42155725},
issn = {2405-4577},
abstract = {BACKGROUND AND AIMS: Intestinal colonization by microbial communities is important for infant health. Little knowledge about the effect of infant formula matrix (i.e. form of protein) on the infant microbiome, is available. The main aim of this study was to investigate how mode of birth, cessation of breastfeeding, and the formula matrix i.e. protein matrix of synbiotic infant formulas modulate intestinal colonization in infants.

METHODS: Stool microbiota profiles of 342 healthy term infants participating in a randomized controlled trial were studied. Infants received synbiotic infant formula manufactured from extensively hydrolyzed (eHF) or intact protein (control formula; CF) as exclusive formula feeding or as mixed feeding (MF) with human milk. Stool samples at 4 and 12 months of age were analyzed by 16S rRNA gene amplicon sequencing.

RESULTS: Phylogenetic profiles of the stool microbiota showed age-dependent maturation. Protein hydrolyzation had only minor effects on overall community types. However, compared to CF, eHF feeding was linked to a Bifidobacterium-dominated microbiota at 4 months of age in two subgroups: in infants born by Cesarean section and those who had received MF for less than 3 months.

CONCLUSION: In this comparison of two synbiotic infant formulas, the formula matrix based on hydrolyzed protein was linked to a Bifidobacterium-dominated community, dependent on birth and feeding mode. Because bifidobacteria are positively linked to infant health and allergy-prevention, further studies are needed to confirm these results and to investigate the effects on clinical outcomes.},
}

@article {pmid42155873,
year = {2026},
author = {Sun, Q and Li, X and Wu, J and Zhang, J and Zhu, Y and Dong, Y},
title = {Immune Checkpoint Inhibitor Resistance in Non-Small Cell Lung Cancer: An Updated View Through the Cancer-immunity Cycle.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105382},
doi = {10.1016/j.critrevonc.2026.105382},
pmid = {42155873},
issn = {1879-0461},
abstract = {Despite the transformative impact of immune checkpoint blockade (ICB) in non-small cell lung cancer (NSCLC), durable responses remain limited to a subset of patients. Resistance-either intrinsic or acquired-continues to undermine the full therapeutic potential of immunotherapy. The cancer-immunity cycle provides a useful conceptual scaffold to dissect the multistep requirements for effective antitumor immunity. Recent advances in single-cell technologies, spatial profiling, longitudinal immune monitoring, and real-world clinical datasets have uncovered additional layers of complexity, including non-canonical pathways involving tumor metabolism, stromal architecture, vascular remodeling, epigenetic plasticity, microbiome-immune crosstalk, and host-related determinants of response. In this review, we provide an updated and integrated synthesis of both primary and acquired resistance mechanisms across each phase of the cancer-immunity cycle. We emphasize pathways that have gained mechanistic or clinical relevance in recent NSCLC literature and consolidate them in an updated reference figure (Figure 1). To strengthen translational relevance, we additionally include a dedicated section on host-related determinants of ICI efficacy-including immunosenescence, performance status, comorbidity burden, systemic inflammation, body composition, and concomitant medications-and a stepwise summary of representative primary versus acquired mechanisms with NSCLC clinical anchors (Table 1). Our goal is to frame resistance not as a single lesion, but as a dynamic tumor-host system that must be mapped to inform biomarker development and rational combination strategies.},
}

@article {pmid42155931,
year = {2026},
author = {Gong, J and Mei, X and Jin, Y and Wang, Y and Liu, Y and Song, W and Wang, Z and Yang, M and Ye, C and Liu, Y and Huang, H and Zhu, S and Deng, W},
title = {Synergistic foliar titanium and soil organic fertilizer drive terpenoid-mediated microbiome assembly to restrict Cd/Pb uptake in Panax notoginseng.},
journal = {Journal of hazardous materials},
volume = {512},
number = {},
pages = {142356},
doi = {10.1016/j.jhazmat.2026.142356},
pmid = {42155931},
issn = {1873-3336},
abstract = {Achieving safe utilization of heavy metal-contaminated soils without compromising crop productivity represents a grand challenge for sustainable agriculture. Although foliar titanium (Ti) and soil organic fertilizers (OF) independently alleviate abiotic stress, it remains unclear whether and how aboveground Ti signaling coordinates with OF mediated rhizosphere processes to enhance crop productivity and restrict heavy metal accumulation through plant-metabolite-microbiome networks. Here, using Panax notoginseng as a model, the results showed that co-application of foliar Ti with soil OF significantly outperformed individual applications. This "top-down" strategy synergistically increased root biomass and saponin content (synergistic index > 1), while reducing root Cd and Pb concentrations by 46.60% and 47.23%, respectively. Mechanistically, soil OF established a functional rhizosphere foundation by enhancing nutrient bioavailability and enriching beneficial microbial taxa. Concurrently foliar Ti acted as a systemic trigger to reprogram plant metabolism, upregulating arginine and proline metabolic pathways in leaves and coinciding with enhanced diterpenoid biosynthesis in roots. Specifically, accumulated diterpenoids (forskolin and ingenol) functioned as selective semiochemicals, recruiting a specialized microbiome consortium with enhanced metal-resistant, growth-promoting, and nutrient-solubilizing bacteria (Sphingomonas, Rhodanobacter, Bacillus) and fungi (Penicillium, Aspergillus), while inhibiting the pathogen Ilyonectria. Consequently, this engineered rhizosphere microbiome may have contributed to rhizosphere-level Cd/Pb exclusion or immobilization, thereby decoupling root metal uptake from bulk soil metal pools. This study supports a novel "aboveground trigger-belowground support" framework in which Ti-induced metabolites promote the assembly of functional microbiomes that are further supported by OF. We propose a targeted biofortification strategy leveraging plant-metabolite-microbiome coordination for safe cultivation of crops.},
}

@article {pmid42155948,
year = {2026},
author = {Yang, W and Li, Z and Chen, X and Chen, J and Lu, Z},
title = {Association between a gut microbiota-targeted dietary index and osteoarthritis/rheumatoid arthritis: a cross-sectional study.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {81},
number = {},
pages = {100995},
doi = {10.1016/j.clinsp.2026.100995},
pmid = {42155948},
issn = {1980-5322},
abstract = {BACKGROUND: Diet plays a key role in regulating the gut microbiota. This study aimed to investigate the association between the Dietary Index of the Gut Microbiome (DI-GM) ‒ a score designed to reflect the potential of a diet to support a healthy gut microbiota ‒ and different types of arthritis, an area where systematic studies remain scarce.

METHODS: Data from the National Health and Nutrition Examination Survey (NHANES) 2007-2018 were analyzed using multivariable logistic regression, Restricted Cubic Spline (RCS) regression, and subgroup analyses to assess associations between DI-GM and Osteoarthritis (OA) and Rheumatoid Arthritis (RA).

RESULTS: A total of 6168 participants were included, among whom 506 had Osteoarthritis (OA) and 303 had Rheumatoid Arthritis (RA). Multivariable analyses showed no significant association between DI-GM and OA (p > 0.05), but significant inverse associations with RA across models (ORs 0.74, 0.64, and 0.74; all p < 0.05). Restricted cubic spline analysis detected no significant nonlinear relationships for either outcome. Subgroup analyses suggested potential associations within certain populations.

CONCLUSION: This cross-sectional study found an inverse association between the diet-based DI-GM score and RA, but no significant association with OA. Given the limitations of the cross-sectional design, the observed association is equally compatible with dietary changes resulting from RA diagnosis and management (reverse causality). As this study did not measure the gut microbiota, the role of the microbiome as a mediator remains speculative. Therefore, these results require confirmation in prospective studies that can account for reverse causation and directly assess the gut microbiome.},
}

@article {pmid42156216,
year = {2026},
author = {Deng, X and Wang, Y and Zhu, H and Guo, Y and Wang, Q and Han, J and Yu, K and Zhou, B},
title = {Metagenomic profiling of resistome and mobilome dynamics in diverse freshwater aquaculture modes.},
journal = {Water research},
volume = {302},
number = {},
pages = {126133},
doi = {10.1016/j.watres.2026.126133},
pmid = {42156216},
issn = {1879-2448},
abstract = {The widespread presence of antibiotic resistance genes (ARGs) in aquaculture environments poses a growing threat to public health. However, comprehensive understanding of ARG distribution and transmission potential across different freshwater aquaculture modes remains limited. This study employed integrated short- and long-read metagenomic sequencing to characterize the resistome, mobilome, and associated microbial communities across three predominant freshwater aquaculture modes (grass carp, crayfish, and crab ponds), using water, sediment, and intestinal samples analyzed at both contig and metagenome-assembled genome (MAG) levels. The results revealed that aquaculture modes and environmental media jointly shaped microbial and ARG compositions. At the contig level, the crayfish system harbored the highest relative abundance of both ARGs and mobile genetic elements (MGEs), with gut samples consistently emerging as the dominant reservoir across all modes. A significant positive correlation between ARG and MGE alpha diversity indicated that the gut microbiome, particularly in crayfish, provides a selective environment that co-enriches resistance genes and their mobile carriers. High-risk core ARGs (Rank I) were at least 19 times more abundant in the crayfish gut than in any other compartment, underscoring the intestinal microbiome as a hotspot for clinically relevant resistance accumulation. At the MAG level, over half of the recovered MAGs met near-complete or high-quality thresholds, and approximately 38% of ARG-carrying MAGs were classified as multidrug-resistant (MDR). MDR MAG abundance was significantly higher in gut than in sediment and water samples, with the crayfish gut as the most enriched compartment. Critically, several crayfish-associated MDR MAGs affiliated with Klebsiella aerogenes carried virulence factor genes (VFGs) and exhibited ARG-MGE-VFG co-localization within prophage sequences, suggesting phage-mediated co-dissemination of resistance and virulence traits. These findings highlight the intestinal microbiome of aquaculture species as a critical hotspot for resistance dissemination and provide a scientific basis for evaluating freshwater aquaculture-associated ARG risks under the One Health framework.},
}

@article {pmid42156361,
year = {2026},
author = {Xiang, N and Liao, T and Xie, M and Wang, Z and Mak, CH and Tang, X and McIlroy, SE and Thibodeau, B and Voolstra, CR and Luo, H},
title = {Decoding coral resistance to eutrophication through the association of hyper‑efficient denitrifiers as key microbial allies.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42156361},
issn = {2041-1723},
support = {GRF14114724//Chinese University of Hong Kong (CUHK)/ ; },
mesh = {*Anthozoa/microbiology/physiology ; Animals ; *Denitrification ; *Eutrophication/physiology ; Coral Reefs ; Nitrates/metabolism ; Hong Kong ; Symbiosis ; Climate Change ; Ecosystem ; Microbiota ; },
abstract = {Coral reefs face a perilous future due to global climate change compounded by the increasing prevalence of local stressors. Prominent among these is nutrient pollution, particularly nitrate eutrophication, which disrupts the coral-algal symbiosis and escalates reef degradation. While microbial denitrification is hypothesized to mitigate nitrate stress, the mechanisms underlying coral resilience remain unknown. Studying Hong Kong's coral "reef oases" that persist under chronic hyper-eutrophication, we discovered that resilience is not mediated by diversity or abundance shifts in denitrifier genera but by the association with specific, hyper-efficient denitrifying populations within the dominant denitrifier genus Ruegeria. By integrating population genomics, subspecies-resolution metabarcoding (resolving both the entire Ruegeria community and the denitrifying sub-community), and direct isotope-based activity assays, we identified and validated putative denitrifying "specialist" populations. These specialists were significantly enriched in corals from high-nitrate waters and exhibited 10-fold higher denitrification rates in low-oxygen incubations, converting nitrate to inert N2 with superior efficiency compared to non-specialists. Our findings reveal that critical ecosystem-scale adaptations to anthropogenic change can occur through a unique association with specialized sub-genus populations, which may be missed in conventional microbiome surveys. As such, our work sheds light into why dominant denitrifying genera are ubiquitous, yet only certain corals thrive in eutrophic conditions. It also provides a framework for future studies delineating ecologically important host-associated microbes.},
}

*Anthozoa/microbiology/physiology
Animals
*Denitrification
*Eutrophication/physiology
Coral Reefs
Nitrates/metabolism
Hong Kong
Symbiosis
Climate Change
Ecosystem
Microbiota

@article {pmid42156377,
year = {2026},
author = {Hu, R and Aronson, HS and Weaver, ME and Price, MN and LaRowe, DE and Liang, Y and Deutschbauer, AM and Coates, JD and Carlson, HK},
title = {Organic carbon oxidation state shapes fermentative methanogenic microbiomes and controls greenhouse gas fluxes.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73281-z},
pmid = {42156377},
issn = {2041-1723},
abstract = {Organic compounds with a negative nominal oxidation state of carbon (NOSC) are thermodynamically recalcitrant in anaerobic ecosystems, but few studies have measured the influence of NOSC on carbon degradation rates, gaseous product yields, or microbiome composition. We amended anaerobic rice paddy sediment microcosms with water-soluble monomeric organic carbon compounds varying in NOSC. Consistent with thermodynamic and stoichiometric predictions, negative NOSC compounds are catabolized more slowly but produce more methane per mole of carbon. Negative NOSC microbiomes have higher alpha diversity, more syntrophs and methanogens, and fewer fermentative bacteria. Strikingly, fermentative bacterial taxa display genomically encoded NOSC catabolic preferences both in the lab and field. Negative NOSC-preferring fermenters have longer predicted doubling times, consistent with the thermodynamic recalcitrance of their preferred substrates. We propose that microbial NOSC catabolic preferences may reflect the thermodynamic niche of microorganisms and we anticipate that extending research on microbial catabolic preferences to a greater variety of organic carbon substrates and diverse microbiomes will improve our understanding of microbial carbon cycling and trait evolution.},
}

@article {pmid42156414,
year = {2026},
author = {Maziers, N and Le Chatelier, E and Plaza Oñate, F and Fromentin, S and Thirion, F and Pons, N and Borruel, N and Casellas, F and Torrejon, A and Robles-Alonso, V and Manichanh, C and Varela, E and Derrien, M and Veiga, P and Oozeer, R and Sunagawa, S and Lombard, V and Terrapon, N and Henrissat, B and , and Guarner, F and Ehrlich, SD},
title = {Fecal microbiome of patients with ulcerative colitis reflects their phenotype and inflammatory level.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-44895-6},
pmid = {42156414},
issn = {2045-2322},
support = {ANR-11-DPBS-0001, MetaGenoPolis (MGP)//Agence Nationale de la Recherche/ ; FP7-HEALTH-F4-2007-201052, MetaHIT//Seventh Framework Programme/ ; },
abstract = {Inflammatory bowel diseases affect ever-increasing numbers of individuals worldwide. Alterations of the intestinal microbiome were reported for Crohn's disease and at relapse in Ulcerative Colitis (UC); they were not clearly detected in UC at remission. Here we report the characterization of the microbiome by quantitative metagenomics in a cohort of 121 individuals, composed of 65 UC adult patients in remission and 56 healthy controls. A cross-sectional comparison revealed substantial microbiome differences, patients in remission having lower microbiome richness and paucity of the Ruminococcus species driven enterotype. The observed microbiome alterations allowed robust classification of patients by intestinal species abundance, yielding an area under the curve (AUC) of 0.87 in a Receiver-Operator Characteristic (ROC) analysis. Loss of richness was linked to an aggressive UC phenotype and to the importance of past relapses; it was associated with a worse IBD quality of life score (IBDQ-36). Unexpectedly, onset of inflammatory bouts, as assessed by white blood cell count and fecal calprotectin levels, was associated with higher richness; in a longitudinal study of patients at high risk of disease flare, we observed a link between increasing gut microbiome richness over time and calprotectin level, in turn related to clinical inflammatory response and relapse.},
}

@article {pmid42156482,
year = {2026},
author = {Weng, J and Hashizume, T and Ying, BW},
title = {Cleaning reshapes bacterial communities in public toilets through disturbance and random reassembly.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-52725-y},
pmid = {42156482},
issn = {2045-2322},
support = {25K02259//Japan Society for the Promotion of Science/ ; },
abstract = {Cleaning of public spaces for human activities is commonly employed and reduces the microbial load in these spaces. However, the mechanisms underlying changes in microbial community structure following cleaning remain poorly understood. As a pilot study, we investigated the bacterial community in public toilets before and after cleaning using 16S rRNA sequencing and computational simulations, as well as bacterial colony growth assays and metabolic functional prediction. The results revealed that cleaning initially imposes a strong disturbance on bacterial communities, followed by continuous stochastic loss and a concurrent influx of bacteria, resulting in changes in community structure. Culturable bacterial communities before and after cleaning showed equivalent growth properties, indicating that cleaning did not alter the original environment. Cleaning time was positively correlated with colony number but not with colony growth capacity, suggesting that bacteria surviving cleaning were fast-growing or highly abundant taxa. Metabolisms related to methane and to diverse environments showed increased contributions to survival after cleaning. Taken together, cleaning-mediated changes in bacterial community structure in public toilets were driven by a stochastic process that renewed bacterial diversity. This study provides new insights into the disturbance and recovery dynamics of the microbiome in public environments subjected to cleaning.},
}

@article {pmid42156647,
year = {2026},
author = {Ravikrishnan, A},
title = {Unlocking the Metagenome: Pipeline for Microbiome Data Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {1-23},
pmid = {42156647},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Metagenome ; *Microbiota/genetics ; *Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; Software ; Workflow ; Sequence Analysis, DNA/methods ; Humans ; Data Analysis ; },
abstract = {Metagenomic technologies have revolutionized our understanding of microbes in different spheres of life, revealing the massive diversity and complex functionalities of microbial communities across various environments. Shotgun metagenomics, which involves sequencing the DNA of all the organisms in a sample, is emerging as a powerful tool in assessing the microbial content. Unlike the traditional culturing approach, the shotgun metagenomic technology provides a comprehensive view of the entire microbial community, including potential functions that the organisms could be performing. In this chapter, we describe a typical bioinformatics workflow to generate the taxonomic profiles from metagenomic sequencing data and demonstrate a few basic statistical analyses that can be performed from this data to generate insights. In addition, we discuss the experimental and analytical considerations that must be taken into account while generating and making inferences from metagenomic data. Lastly, we provide insights on automating the workflow for consistent and reproducible large-scale analyses.},
}

*Metagenomics/methods
*Metagenome
*Microbiota/genetics
*Computational Biology/methods
High-Throughput Nucleotide Sequencing/methods
Software
Workflow
Sequence Analysis, DNA/methods
Humans
Data Analysis

@article {pmid42156648,
year = {2026},
author = {Yugandhar Reddy, BS and Sripradha, S and Kumar, A},
title = {Targeted Metagenomics Using Next-Generation Sequencing Methods.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {25-32},
pmid = {42156648},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Microbiota/genetics ; Metagenome ; Humans ; Sequence Analysis, DNA/methods ; },
abstract = {Metagenomics allows the discovery of the full diversity of all microbes present in a given niche. The technique is very powerful and has allowed very significant advances delineating the role of the microbiome in several disciplines including health, agriculture, ecology, industry, etc. Here, we describe the method required for processing of samples for metagenomic analysis using Next-Gen sequencing.},
}

*Metagenomics/methods
*High-Throughput Nucleotide Sequencing/methods
Microbiota/genetics
Metagenome
Humans
Sequence Analysis, DNA/methods

@article {pmid42156649,
year = {2026},
author = {Rangamaran, VR and Sushmitha, TJ and Tamilmani, KK and Murugesan, H and Gopal, D},
title = {Exploring the Ocean's Microbial World: Techniques and Protocols for Microbiome Research.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {33-46},
pmid = {42156649},
issn = {1940-6029},
mesh = {*Microbiota/genetics ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Oceans and Seas ; *Seawater/microbiology ; Computational Biology/methods ; },
abstract = {Marine microbiomes play a crucial role in oceanic ecosystems, influencing biogeochemical cycles, climate regulation, and marine biodiversity. Accurate characterization of these microbial communities requires standardized protocols for sample collection, processing, sequencing and data analysis. This chapter provides a comprehensive guide to essential methodologies for marine microbiome research including field sampling strategies, DNA and RNA extraction techniques, high-throughput sequencing approaches (such as 16S rRNA amplicon sequencing and metagenomics) and bioinformatics pipelines for data interpretation. Additionally, we discuss quality control measures, best practices for reproducibility, and challenges associated with marine microbiome profiling. By adopting standardized methodologies, researchers can generate reliable, comparable datasets that enhance our understanding of marine microbial ecology and its broader environmental implications.},
}

*Microbiota/genetics
*Metagenomics/methods
High-Throughput Nucleotide Sequencing/methods
RNA, Ribosomal, 16S/genetics
Oceans and Seas
*Seawater/microbiology
Computational Biology/methods

@article {pmid42156651,
year = {2026},
author = {Jiménez, DJ and Díaz-García, L and Aldakheel, L and Rosado, AS},
title = {Dilution-to-Stimulation: A Method for Selecting Polymer-Transforming Microbial Consortia.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {75-81},
pmid = {42156651},
issn = {1940-6029},
mesh = {*Microbial Consortia ; Soil Microbiology ; *Polymers/metabolism ; },
abstract = {The utilization of liquid enrichment cultures for selecting microbial communities has been employed to recover and increase the abundance of desired microbes capable of thriving on specific carbon sources. This strategy facilitates the development of microbial consortia designed to serve as models for studying the eco-enzymology of particular metabolic processes. In this context, we introduce a top-down method referred to as "dilution-to-stimulation" to artificially select polymer-transforming microbial consortia from soil samples.},
}

*Microbial Consortia
Soil Microbiology
*Polymers/metabolism

@article {pmid42156652,
year = {2026},
author = {Kosmopoulos, JC and Anantharaman, K},
title = {Computational Microbial and Viral Ecology Analysis.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {83-141},
pmid = {42156652},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; *Computational Biology/methods ; Metagenome ; *Microbiota/genetics ; *Viruses/genetics/classification ; Virome ; Bacteriophages/genetics ; Bacteria/genetics ; Archaea/genetics ; },
abstract = {The explosion in known microbial diversity in the last two decades has made it abundantly clear that microbes in the environment do not exist in isolation; they are members of communities. Accordingly, omics approaches such as metagenomics have revealed that interactions between diverse groups of community members such as archaea, bacteria, and viruses (bacteriophages) are common and have significant impacts on entire microbiomes. Thus, to have a well-developed understanding of microbes as they naturally exist in the environment, biological entities of all kinds must be studied together. While numerous protocols for metagenome analysis exist, comprehensive published protocols for the simultaneous analysis of viruses and prokaryotes together are scarce. Further, as bioinformatic methods for microbiology rapidly advance, existing metagenomic tools and pipelines require frequent re-evaluation. This ensures the adherence to best practices for microbiome and metagenomic data analysis. Here, we offer an expansive approach for the joint analysis of bulk sequence data from a mixed microbial community (metagenomes) and viral-sized fraction communities (viromes). This chapter serves as a beginner's-level guide for researchers with limited bioinformatics expertise who wish to engage in multiscale metagenome and virome analyses. We cover steps from initial study design to sequence read processing, metagenome assembly, quality control, virus identification, microbial and viral genome binning, taxonomic characterization, species-level clustering, and host-virus predictions. We also provide the bioinformatic scripts used in our workflow for reuse in one's own computational methods. Lastly, we discuss additional approaches a researcher can take after processing data with this workflow.},
}

*Metagenomics/methods
*Computational Biology/methods
Metagenome
*Microbiota/genetics
*Viruses/genetics/classification
Virome
Bacteriophages/genetics
Bacteria/genetics
Archaea/genetics

@article {pmid42156653,
year = {2026},
author = {Bhusan, KK and Bose, T and Dutta, A},
title = {Identifying Differential Network Properties and Driver Microbes in Microbial Association Networks Using CompNet and NetShift.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {143-165},
pmid = {42156653},
issn = {1940-6029},
mesh = {*Microbiota ; *Software ; *Computational Biology/methods ; Microbial Interactions ; Bacteria/genetics ; Humans ; },
abstract = {This chapter describes CompNet and NetShift, two network analysis tools, which can help in comparison and analysis of microbial association networks. Biological interaction networks are basic representations of entities present in a biological system and their inter-relationships, which lies at the foundation of any modeling approaches. Inter-microbial associations define the community structure of a given microbiome and understanding these interaction networks are pivotal to modeling the microbiome. CompNet helps in the comparison of various network properties across multiple different microbial association networks that may represent communities inhabiting different/contrasting environments. NetShift helps in the identification of key microbes (driver organisms) in the network that can drive changes in community composition and interactions (network topology) characteristic of communities residing in different environments.},
}

*Microbiota
*Software
*Computational Biology/methods
Microbial Interactions
Bacteria/genetics
Humans

@article {pmid42156654,
year = {2026},
author = {Sambamoorthy, G and Ansari, AF and Dixit, NM},
title = {Estimating Effective Pairwise Interactions to Predict the Structures of Microbial Communities (EPICS).},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {167-174},
pmid = {42156654},
issn = {1940-6029},
mesh = {*Microbiota ; *Microbial Interactions ; Algorithms ; },
abstract = {The engineering of multispecies microbial communities is important to applications in healthcare, biotechnology, and environmental sustainability. Predicting the structures of such communities requires knowledge of the interactions between the species involved. When high-order interactions are present, bottom-up approaches, which rely on the assembly of all possible subcommunities, become prohibitive because the number of such subcommunities scales exponentially with the number of species. Here, we present an alternative, top-down approach, EPICS, which requires the assembly of subcommunities whose number scales linearly with the number of species, hugely reducing experimental effort. EPICS estimates effective pairwise interactions between species, which subsume high-order interactions, using data from monocultures and leave-one-out subcommunities and predicts community structures. The method is efficient and scalable to large communities.},
}

*Microbiota
*Microbial Interactions
Algorithms

@article {pmid42156658,
year = {2026},
author = {Roma Pi, J and Heinken, A},
title = {Personalized Constraint-Based Modeling of Microbial Communities from Metagenomic Data.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {233-260},
pmid = {42156658},
issn = {1940-6029},
mesh = {*Metagenomics/methods ; Humans ; *Gastrointestinal Microbiome/genetics ; Precision Medicine/methods ; Software ; *Microbiota/genetics ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Systems Biology/methods ; },
abstract = {High-throughput metagenomic sequencing techniques such as 16S rRNA and shotgun sequencing have enabled an unprecedented understanding of the structure and function of microbiome communities such as the human gut microbiome. Tailored dietary or therapeutic interventions targeting the microbiome could advance personalized medicine; however, predicting such interventions requires predictive systems biology methods. Constraint-Based Reconstruction and Analysis (COBRA) is a mechanistic systems biology approach that relies on detailed genome-scale reconstructions of a target organism's metabolism. A resource of genome-scale reconstructions of human microbes, AGORA, and its expansion in size and scope, AGORA2, have been developed through a semi-automated refinement pipeline, DEMETER. A user-friendly analysis pipeline, mgPipe, allows building and interrogating personalized models of microbiome communities from AGORA and AGORA2. Through sample-specific simulations, mgPipe can stratify patients and controls by the distinct metabolic capabilities of their microbiomes, starting from the processed metagenomic sequencing data. Building on this functionality, the protocol provides a comprehensive workflow for the contextualization of metagenomics data through personalized, mechanistic modeling. Comprehensive tutorials for the DEMETER and mgPipe workflows are presented, which will enable both systems biologists and microbiome scientists to contextualize metagenomic data and perform mechanistic simulations of diet-microbiome-host interactions.},
}

*Metagenomics/methods
Humans
*Gastrointestinal Microbiome/genetics
Precision Medicine/methods
Software
*Microbiota/genetics
*Metagenome
High-Throughput Nucleotide Sequencing/methods
Computational Biology/methods
RNA, Ribosomal, 16S/genetics
Systems Biology/methods

@article {pmid42156661,
year = {2026},
author = {Nawaz, A and Schaefer, JL and Centler, F},
title = {Dynamic Simulation of Growth and Cross-Feeding in Microbiomes with μbialSim.},
journal = {Methods in molecular biology (Clifton, N.J.)},
volume = {3006},
number = {},
pages = {317-330},
pmid = {42156661},
issn = {1940-6029},
mesh = {*Microbiota ; Computer Simulation ; Software ; *Models, Biological ; Microbial Interactions ; Bioreactors/microbiology ; Computational Biology/methods ; },
abstract = {Microbial cells in natural environments are typically embedded in microbial communities consisting of few to many different species. Close proximity and high diversity of neighboring cells facilitate manifold interactions on several layers, from substrate competition, exchange of genetic material, to metabolic cross-feeding. The complexity of these ecological interaction networks makes microbiomes notoriously difficult to study. While microbiome dynamics can routinely be elucidated by meta-omics technologies, pinpointing mechanisms driving these observed dynamics remains a challenge. Mechanistic mathematical modeling with its ability to focus on individual interactions and exploring their isolated impact on overall dynamics has emerged as a suitable tool in this context. Here, we use μbialSim, an open-source simulator that extends the Flux Balance Analysis approach to microbial communities, considering substrate competition and metabolic cross-feeding but neglecting any other microbial interactions. Assuming a well-mixed bioreactor environment, simulated trajectories enable the analysis of growth behavior of individual microbiome members, dynamics of intracellular enzymatic fluxes across all species, as well as the analysis of cross-feeding behavior and how it changes over time. The MATLAB implementation of μbialSim is available from https://github.com/fcentler/microbialSim .},
}

*Microbiota
Computer Simulation
Software
*Models, Biological
Microbial Interactions
Bioreactors/microbiology
Computational Biology/methods

@article {pmid42156754,
year = {2026},
author = {Zhao, T and Li, B and Liu, Y and Zhang, J and Fan, X and Ao, M and Niu, Y and Li, D and He, J and Sun, D and Wu, H and Tang, T and Liu, Z and Huang, X},
title = {Enterococcus hirae QT4713-derived dopamine ameliorates intestinal inflammation and MPTP-induced Parkinson's disease in mice.},
journal = {NPJ Parkinson's disease},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41531-026-01392-x},
pmid = {42156754},
issn = {2373-8057},
support = {32200782//National Natural Science Foundation of China/ ; },
abstract = {Gut microbiota dysbiosis contributes to Parkinson's disease (PD) pathology by altering dopamine metabolism in the gut-brain axis. Although probiotics and other functional strains have been proposed as microbiome-based interventions, few naturally occurring gut microbes show therapeutic potential for PD. Here, we isolated Enterococcus hirae QT4713 (QT4713) from the hypoxic, low-pressure Qinghai-Tibet Plateau (4713 m altitude). Whole-genome sequencing revealed that QT4713 harbors a tyrosine decarboxylase gene (TyrDc), enabling conversion of L-tyrosine to dopamine in vitro. In mice, QT4713 enhanced antioxidant enzyme activity, reduced inflammatory mediators, reshaped gut microbial composition, and promoted short-chain fatty acid production. Metabolomic analyses indicated activation of L-tyrosine metabolism, with increased L-DOPA and dopamine levels in the colon and feces, accompanied by improved motor performance. In an MPTP-induced PD mouse model, QT4713 alleviated motor and gastrointestinal dysfunction, reduced oxidative and inflammatory damage, and attenuated dopaminergic neuron loss. QT4713 also increased dopamine and tyrosine levels in the striatum. Extending beyond an acute toxin model, QT4713 partially rescued PD-like phenotypes in TMEM175 knockout mice, preserving tyrosine hydroxylase-positive neurons in the substantia nigra. Together, these findings suggest that QT4713 can mitigate gastrointestinal disturbances and other PD-related deficits, consistent with combined effects on catecholamine-related metabolism and gut microbiota remodeling.},
}

@article {pmid42156769,
year = {2026},
author = {Chen, R and Luo, S and Feng, Y and Maestre, FT and Sáez-Sandino, T and Gross, N and Le Bagousse-Pinguet, Y and Ochoa, V and Gozalo, B and Guirado, E and García-Gómez, M and Valencia, E and Asensio, S and Martínez-Valderrama, J and Mendoza, BJ and Abades, S and Alfaro, F and Barrett, M and Berdugo, M and Pastor, JLB and Blaum, N and Boldgiv, B and Bowker, M and Castro, H and Chu, H and Cutler, NA and Dai, Z and Deák, B and Durán, J and Espinosa, CI and Fajardo, A and Fan, K and Foronda, A and Fraser, LH and Geissler, K and Grebenc, T and Moltanvan, EG and Hart, SC and Kindermann, L and Köbel, M and Laanisto, L and le Roux, PC and Liancourt, P and Linstädter, A and Louw, MA and Macek, P and Maggs-Kölling, G and Makhalanyane, TP and Manzaneda, AJ and Marais, E and Montesinos, D and Mora, JP and Moreno, G and Munson, SM and Muñoz-Rojas, M and Nair, GR and Neuhauser, S and Nunes, A and Plaza, C and Pueyo, Y and Rey, PJ and Rey, A and Ríos, AL and Rodríguez, A and Lozano, BR and Roman, R and Ruppert, JC and Salah, A and Singh, J and Throop, HL and Travers, S and Nahberger, TU and Uuganbayar, M and Valkó, O and Wang, L and Williams, MA and Xiong, C and Xu, J and Zaady, E and Ma, B and Singh, BK and Delgado-Baquerizo, M},
title = {Functional restructuring of the global soil microbiome under multiple stressors.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73231-9},
pmid = {42156769},
issn = {2041-1723},
support = {42577352//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Microbes, as the planet's most abundant and diverse organisms, drive soil functions globally and are vulnerable to environmental stressors triggered by global change. Yet, knowledge regarding the impacts of multiple environmental stressors on their functional profiles as well as the consequences for soil functionality largely remains unknown. Here, we analyze two global-scale datasets including information on soil metagenomics and multiple environmental stressors. We find that across terrestrial ecosystems worldwide, up to 60% of all functional genes significantly shift when soil microbes experience the high-level of concurrent stressors. In this regard, the relative abundances of genes involved in microbial growth are negatively linked to the increasing number of stressors. Conversely, those genes linked to stress resistance and energy production exhibit positive responses. Taken together, our findings highlight a significant restructuring of global soil functional microbiomes in response to multiple environmental stressors. Consequently, such restructuring drives community-level shifts in matter and energy reallocations, thereby impacting the maintenance of soil functionality under the projected global change.},
}

@article {pmid42156772,
year = {2026},
author = {Bamberger, T and Muller, E and Algavi, YM and Greenier, A and Adjangba, C and Slikas, E and Brassington, L and Mariner, B and McCoy, B and Harrison, BR and Partida-Aguilar, M and Marye, A and Harris, A and Rout, E and , and Avery, A and Promislow, DEL and Snyder-Mackler, N and Borenstein, E},
title = {Mapping the canine gut microbiome: insights from the Dog Aging Project.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73193-y},
pmid = {42156772},
issn = {2041-1723},
support = {U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; U19AG057377//U.S. Department of Health & Human Services | NIH | National Institute on Aging (U.S. National Institute on Aging)/ ; },
abstract = {Companion dogs (Canis lupus familiaris) offer a unique model for studying the gut microbiome and its relation to aging due to their cohabitation with humans, sharing similar environments, diets, and healthcare practices. Here, we present the Dog Aging Project (DAP) Precision cohort, a large population-wide study of the canine gut microbiome. This cohort encompasses over 900 dogs of diverse breeds, environments, and demographics living across the United States. Coupling fecal shotgun metagenomic sequencing with phenotypic and environmental surveys and clinical lab tests, we explore the intricate relationships between microbiome composition, aging, and key factors such as health and living conditions. Our analyses identify multiple factors associated with microbiome composition, including dietary preferences such as commercial versus home cooked nutrition, and behaviors such as coprophagy (feces eating). In addition, we find age-associated gradual shifts in microbiome composition, supporting the development of a metagenomics-based population-level model for canine age prediction based on microbial signatures. We further examined which age-associated microbial patterns observed in humans are recapitulated in dogs by comparing our cohort with the Lifelines-DEEP cohort. Overall, these findings offer insights into the role the gut microbiome plays in our four-legged companions, with potential implications for veterinary medicine and translational aging research.},
}

@article {pmid42156980,
year = {2026},
author = {Wiest, IC and Dreikhausen, L and Keller, R and Marin-Galiano, M and Albiges, L and Meran, J and Leucht, K and Rieken, S and Esteban, E and Zengerling, F and Tintelnot, J and Grimm, MO and Bozorgmehr, F and Christopoulos, P and Stein, A and Binder, M and Härtel, N and Klinghammer, K and Grünwald, V and Pogorzelski, M and Ebert, MP},
title = {Differential effects of prior versus concomitant Steroid and Antibiotic Treatment on Immunotherapy Efficacy - A Pooled Analysis of the RAMONA, INTEGA, OPTIM, ELDORANDO, FORCE, TITAN-RCC and TITAN-TCC Trials of the German AIO Study Group.},
journal = {British journal of cancer},
volume = {},
number = {},
pages = {},
pmid = {42156980},
issn = {1532-1827},
abstract = {BACKGROUND: We explored the association of immune-related adverse events (irAE), along with prior and concomitant antibiotic and steroid use, on oncological outcomes following immune checkpoint inhibitor (ICI) treatment in various solid tumours.

METHODS: Pooled data from seven trials on ICI therapy across multiple cancer types (head and neck, non-small cell lung cancer, gastroesophageal junctional adenocarcinoma, oesophageal, renal cell, and urothelial carcinoma) was analysed, focusing on overall survival (OS) and progression-free survival (PFS) and antibiotic or steroid use before and during the study.

RESULTS: Of 693 patients, 80 used steroids and 52 used antibiotics prior to the study, while 360 and 331, respectively, used them concomitantly. Lack of prior antibiotic use was associated with longer OS (No vs. Yes: HR 0.552, 95%-CI 0.370-0.822, p = 0.0035) and PFS (No vs. Yes: HR 0.703, 95%-CI 0.485-1.019, p = 0.0625), whereas concomitant antibiotic use had no such effect. Patients with concomitant steroid use demonstrated longer PFS (No vs. Yes: HR 1.359, 95%-CI 1.091-1.693, p = 0.0061).

DISCUSSION: Our study confirmed associations between antibiotic and steroid use and ICI efficacy in cancer. Prior, but not concomitant, antibiotic use was linked to reduced OS, supporting the role of microbiome diversity in tumour response. Concomitant steroid use was associated with improved PFS, potentially reflecting its link to irAE occurrence.},
}

@article {pmid42157054,
year = {2026},
author = {Cheng, S and Hao, X and Liu, S and Zhang, L and Zhang, S and Chen, Y and Wang, L and Xin, S and Li, Z and Hua, Z and Cao, H},
title = {Integrated multi-omics analysis reveals a gut microbiota-tryptophan metabolism axis contributes to sex differences in a β-aminopropionitrile-induced aortic dissection mouse model.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00925-6},
pmid = {42157054},
issn = {2042-6410},
support = {LHGJ20240212//the joint construction project of Medical Science and Technology Research Plan of Henan Province/ ; 82300717//the National Natural Science Foundation of China/ ; HNCMS202420//the Clinical Medical Scientist Training Program of Henan Province/ ; },
abstract = {BACKGROUND: Sex differences in aortic dissection (AD) have been consistently reported in epidemiological studies and experimental mouse models, with males showing markedly higher susceptibility. However, the molecular basis underlying these sex-specific differences remains insufficiently understood.

METHODS: Three-week-old male and female C57BL/6J mice were administered 0.4% β-aminopropionitrile (BAPN) in drinking water for 28 d to induce AD. After the induction period, fecal samples, serum, and aortic tissues were collected from all surviving animals. Integrated analyses included strand-specific transcriptomic sequencing of aortic tissues, untargeted serum metabolomics, and full-length 16 S rRNA sequencing of fecal samples to characterize sex-related differences across transcriptomic, metabolic, and microbiome layers. Inter-omics correlations were further assessed using bioinformatic approaches. Furthermore, in vivo experiments were conducted to validate the impact of key metabolites on the progression of AD.

RESULTS: Female mice exhibited significantly lower susceptibility to BAPN-induced AD, including reduced rates of aortic rupture, lower incidence of AD or aneurysm (AAD), and attenuated aortic dilation. Transcriptomic analysis revealed that female non-dissected mice (FeNonAD) displayed diminished induction of inflammation-related genes and lower predicted immune cell infiltration. Metabolomic profiling revealed significant elevations of tryptophan-indole pathway metabolites-such as indolepyruvate, indole-3-acetic acid, and indolepropionic acid-in both FeNonAD and AAD groups. Microbiome analysis further revealed a higher relative abundance of tryptophan-metabolizing taxa, particularly key Clostridium species, in the intestinal tract of FeNonAD mice, accompanied by significant upregulation of key functional genes (tyrB and aspC) associated with indolepyruvate synthesis. Weighted gene co-expression network analysis (WGCNA)-based integration identified strong negative correlations between indolepyruvate and indole-3-acetic acid sodium salt levels and aortic gene modules linked to immune-inflammatory activation. Further in vivo experiments demonstrated that treatment with indolepyruvate delayed AD progression in male mice.

CONCLUSION: This study highlights a central "gut microbiota-tryptophan metabolism-aortic inflammation" axis that contributes to sexual dimorphism in BAPN-induced AD. These findings provide new molecular insights into sex-specific disease mechanisms and offer a conceptual basis for developing sex-tailored diagnostic and therapeutic strategies.},
}

@article {pmid42157110,
year = {2026},
author = {Al Achkar, N and Privitera, GF and Arena, D and Nicotra, R and Ciccarello, L and Rizzo, GF and Pulvirenti, A and Spatafora, M and Restuccia, C and Branca, F},
title = {Exogenous microbial consortia modulate rhizosphere microbiome and yield of grafted tomato grown in the mediterranean greenhouse.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-08962-4},
pmid = {42157110},
issn = {1471-2229},
support = {CN00000022//AGRITECH National Research Center (European Union Next-Generation EU, PIANO NAZIONALE DI RIPRESA E RESILIENZA, PNRR - MISSIONE 4 COMPONENTE 2, INVESTIMENTO 1.4-D.D. 1032 17/06/2022)/ ; },
abstract = {BACKGROUND: The adoption of sustainable agricultural practices for intensive horticultural production could determine less damage to the ecosystem is a fundamental need increasing worldwide. In this trial the effect of two commercial microbial consortia, applied on two hybrid rootstocks of tomato grafted by two scions, were evaluated both on yield components and on the compositions of the rhizosphere microbiome. The rhizosphere was collected from each grafting combination, in both treated and non-treated plots. Microbiome DNA extracted was then sequenced by amplifying two specific regions ITS1-1F for fungus and 16SV34 for bacteria.

RESULTS: At the morphological level, the effect of microbial consortia application on the total production and yield showed to be highly dependent on the grafting combination, yield increased by 9.1, 10.3 and 12.6% in treated plots of Auto S2, R1/S1 and R1/S2 respectively but registered a reduction of 22.4% in NG.S2 and 9.3% in R2/S2 plots. The metagenomic sequencing revealed that fungal community composition was significantly influenced by both grafting combinations and microbial treatments (especially on the relative abundance of major phyla; Ascomycota and Basidiomycota), whereas bacterial communities exhibited stronger shifts in response to microbial consortia application than to grafting combinations. Correlation analysis between the rhizosphere microbial taxa, yield, and root weight highlighted significant associations supporting the potential of combined use of these practices. Notably, although the inoculated microorganisms were detected at low abundance or were not detectable in treated soils, pronounced shifts in the overall microbiome structure were observed, suggesting indirect yet significant ecological effects of the consortia.

CONCLUSION: This study demonstrates that microbial consortia and grafting synergistically enhance tomato productivity and modulate rhizosphere microbial communities in the monoculture degraded soil under intensive Mediterranean greenhouse conditions. These findings advance current understanding of plant genotype × microbial consortium interactions by demonstrating that microbial inoculant relevant effects are highly modulated by plant genotype and can indirectly restructure rhizosphere microbial assemblages, contributing to the development of more sustainable and resilient horticultural systems.},
}

@article {pmid42157234,
year = {2026},
author = {Shi, Y and Rao, Z and Liu, C and She, M and Yu, Y and Zhu, J},
title = {Microbial enterotype is linked to episodic and working memories via brain function in the parietal and occipital cortices.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02635-2},
pmid = {42157234},
issn = {1741-7007},
abstract = {BACKGROUND: Classification of human gut microbiome into distinct enterotypes based on gut microbial community composition has provided an attractive framework for population stratification. While empirical evidence indicates that microbial enterotype is related to brain function and memory, the neural processes underlying this interaction remain to be further characterized.

RESULTS: In 510 healthy young adults, we used 16S rDNA amplicon sequencing to perform enterotyping, acquired resting-state functional MRI data to calculate brain functional measures, and assessed both episodic and working memories. Inter-enterotype differences in brain functional measures were examined, followed by performance of correlation and mediation analyses to disentangle the potential associations between enterotype, brain function, and memory. We found significant differences in multiple brain functional measures in the parietal and occipital cortices across Bacteroides, Prevotella, and Ruminococcaceae enterotypes. Moreover, these differential brain functional measures were correlated with both episodic and working memories, and further mediated the relationship between enterotype and memory.

CONCLUSIONS: Our findings not only establish brain function as the mediating factor between enterotype and memory, but also hold translational potential for informing novel treatment for cognitive dysfunction via targeting the microbiota-gut-brain axis.},
}

@article {pmid42157265,
year = {2026},
author = {Zia, B and AlKaabi, J and Agha, A and Sharma, C and Ali, BR},
title = {The diabetes exposome: interplay of environmental and genetic determinants in diabetes.},
journal = {Human genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40246-026-00987-y},
pmid = {42157265},
issn = {1479-7364},
support = {NP-25-05//College of Medicine and Health Sciences, United Arab Emirates University/ ; 12R270//United Arab Emirates University/ ; },
abstract = {Diabetes mellitus arises from complex interactions between biological susceptibility and diverse environmental influences that extend beyond traditional "genes versus lifestyle" models. The exposome is defined as the aggregate of non-genetic environmental exposures and their biological consequences across the life course. It provides a systems-level framework to evaluate this interaction, spanning chemical, physical, social, and behavioral domains while integrating them with internal molecular responses to decode how environments shape metabolic health. Emerging assessment strategies, including exposome-wide association studies (ExWAS), high-resolution mass spectrometry-based biomonitoring, geospatial and remote-sensing platforms, and wearable exposure sensors, enable characterization of multi-exposure profiles rather than single agents in isolation. Within exposome domains, air pollution, endocrine-disrupting chemicals, food-borne contaminants, exposome characteristics of the built environment, and chronic psychosocial stress have each been shown to contribute to the development and progression of both type 1 and type 2 diabetes. These diverse exposures often share common pathogenic mechanisms of chronic low-grade inflammation, oxidative and nitrosative stress, alterations in the gut microbiome, and epigenetic changes that ultimately lead to glucose dysregulation. Recent progress in metabolomics, lipidomics, and epigenomics is elucidating the "internal exposome," providing molecular fingerprints that encode prior exposure and detect early metabolic disruption. This integrated approach argues for a paradigm adjustment in diabetes prevention from behavior-centered strategies to those that also target upstream environmental determinants. Exposomic information can improve risk prediction, inform precision public health and medical practice, and inform policy regarding air pollution, chemical use, urban planning, and food systems. This review summarizes the current state of knowledge of the exposome in diabetes, describing its conceptual underpinnings, major tools of assessment, major epidemiologic findings, and biological mechanisms, and identifying the key challenges and opportunities for exposomics to inform effective approaches to diabetes prevention and planetary health.},
}

@article {pmid42157342,
year = {2026},
author = {Jing, Y and Liu, S and Leng, L and He, J and Wang, T and Guan, Y and Su, Z and Zhang, W and Li, Y and Luan, P and Cheng, B and Wang, N and Li, H},
title = {Microbiota transplantation and multi-omics profiling integration unveil the mechanism of Alistipes communis-driven abdominal fat deposition in chickens.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42157342},
issn = {1674-9782},
support = {No. 2022YFF1000201//National Key Research and Development Program of China/ ; No. NK20221001//National Major Agricultural Science and Technology Project/ ; No. 32272863//National Natural Science Foundation of China/ ; No. CARS-41//The earmarked fund for CARS-41/ ; },
abstract = {BACKGROUND: Emerging evidence highlights strong correlations between the cecal microbiome and abdominal fat deposition (AFD) in chickens. However, the specific microbial species driving this process remain unclear. This study aims to identify the key microbe and elucidate its underlying mechanism in regulating chicken AFD.

RESULTS: First, cecal microbiota transplantation confirmed a causal relationship between the cecal microbiota and AFD. Subsequently, metagenomic and metatranscriptomic integrations identified Alistipes communis as a key microbe implicated in AFD. Finally, in vivo gavage integrated with multi-omics revealed that A. communis enhances AFD by disrupting host tryptophan and histidine metabolism. This was evidenced by the elevated concentrations of amino acid metabolism-related metabolites, including L-phosphoarginine and spermine in the cecum.

CONCLUSIONS: This study provides direct evidence that the cecal microbiome serves as a key driver in chicken AFD and identifies A. communis as a critical AFD regulator, offering valuable insights into the gut microbiome's role in host obesity.},
}

@article {pmid42157481,
year = {2026},
author = {Garvey, K and Harris, JK and Furuta, GT and Occhipinti, KA and Wagner, BD and Fernandez, J and VeDepo, M and Fouquier, J and Hill, EB and Robertson, CE and Ackerman, S and Shandas, R},
title = {Minimally invasive capsule-string device enables spatially resolved microbiome profiling across the upper gastrointestinal tract.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2675764},
doi = {10.1080/19490976.2026.2675764},
pmid = {42157481},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Bacteria/classification/genetics/isolation & purification ; Adult ; Male ; Female ; *Upper Gastrointestinal Tract/microbiology ; Middle Aged ; Young Adult ; Stomach/microbiology ; Esophagus/microbiology ; },
abstract = {Regional variation in the human gastrointestinal microbiome remains difficult to characterize because existing sampling methods either rely on invasive endoscopy or stool, which poorly reflects the upper gut. We evaluated a minimally invasive capsule-string device capable of collecting luminal and mucosal material from the esophagus, stomach, duodenum, and jejunum during natural transit. In healthy adults, compartment-level samples were anatomically localized using pH, bile staining, and string length, and microbial communities were profiled by 16S rRNA gene sequencing. The device was well tolerated and consistently recovered sufficient biomass from all upper GI regions. Distinct microbial signatures were evident across compartments, with the strongest differences observed between proximal (esophageal and gastric) and small-intestinal communities. Although the individual host exerted the dominant influence on the overall community structure, a reproducible regional signal persisted after accounting for between-person variation. These findings demonstrate that capsule-string sampling provides reliable access to spatially resolved upper GI microbiota without endoscopy. This approach enables more precise mapping of gut microbial organization in vivo and creates new opportunities for longitudinal, mechanistic, and disease-focused studies of host‒microbiome interactions in regions that have historically been inaccessible.},
}

Humans
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
*Bacteria/classification/genetics/isolation & purification
Adult
Male
Female
*Upper Gastrointestinal Tract/microbiology
Middle Aged
Young Adult
Stomach/microbiology
Esophagus/microbiology

@article {pmid42157498,
year = {2026},
author = {Menadi, S and Cacan, E},
title = {Synergistic Anticancer Effects of Akkermansia muciniphila Combined With 5-Fluorouracil Through BAX/BCL2 Dependent Apoptosis in Colorectal Cancer Cells.},
journal = {Cell biochemistry and function},
volume = {44},
number = {5},
pages = {e70234},
doi = {10.1002/cbf.70234},
pmid = {42157498},
issn = {1099-0844},
support = {//Bilimsel Arastirma Projeleri/ ; },
mesh = {Humans ; *Fluorouracil/pharmacology ; *Apoptosis/drug effects ; *Colorectal Neoplasms/pathology/drug therapy/metabolism ; *bcl-2-Associated X Protein/metabolism/genetics ; *Proto-Oncogene Proteins c-bcl-2/metabolism/genetics ; *Akkermansia ; Drug Synergism ; Cell Survival/drug effects ; *Antineoplastic Agents/pharmacology ; Cell Line, Tumor ; },
abstract = {Colorectal cancer (CRC) continues to be one of the deadliest cancers worldwide, mainly due to late diagnosis, chemoresistance, and the complex interactions within the tumor microenvironment. Recent studies suggest that the gut bacterium Akkermansia muciniphila plays a key role in maintaining intestinal health and may influence the effectiveness of cancer therapies. Therefore, the main aim of this study was to explore whether a lyophilized form of A. muciniphila could support CRC treatment. First, we analyzed A. muciniphila abundance in healthy, adenoma, and CRC tissues using public datasets. Next, CRC cell lines (HT29, HCT116, and SW620) and normal stromal cells (Hs738 St/Int) were treated with increasing doses of the bacterial extract, alone and with 5-fluorouracil (5-FU). Then, cell viability measured by MTT assay, apoptosis by BAX/BCL2 expression via RT-qPCR, and physicochemical properties by zeta potential analysis. The results showed a marked reduction of A. muciniphila abundance in CRC samples, with an early decline from healthy to adenoma tissues and a slight recovery in advanced tumors. In vitro, the extract demonstrated dose-dependent cytotoxicity toward cancer cells, with HT29 showing strong sensitivity at low doses, HCT116 responding at higher concentrations, and SW620 exhibiting greater resistance. Importantly, the extract was well tolerated by normal cells, unlike 5-FU. Combining the extract with 5-FU resulted in a synergistic effect, indicating the possibility of reducing 5-FU dosage to limit its toxicity. The extract significantly upregulated BAX, downregulated BCL2, and displayed strong negative zeta potential, supporting enhanced apoptotic activation and selective interaction with cancer cell membranes. These findings suggest that A. muciniphila and its derived products may serve as promising adjuncts in personalized microbiome-based CRC therapy.},
}

Humans
*Fluorouracil/pharmacology
*Apoptosis/drug effects
*Colorectal Neoplasms/pathology/drug therapy/metabolism
*bcl-2-Associated X Protein/metabolism/genetics
*Proto-Oncogene Proteins c-bcl-2/metabolism/genetics
*Akkermansia
Drug Synergism
Cell Survival/drug effects
*Antineoplastic Agents/pharmacology
Cell Line, Tumor

@article {pmid42157503,
year = {2026},
author = {Ponsero, AJ and Bahcivanci, B and Hayhoe, A and Acharjee, A and Özkurt, E},
title = {The human gut microbiome across the life course.},
journal = {FEBS letters},
volume = {},
number = {},
pages = {},
doi = {10.1002/1873-3468.70361},
pmid = {42157503},
issn = {1873-3468},
support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; },
abstract = {Across the human lifespan, the gut microbiome exhibits considerable inter-individual variation. However, individuals within the same age group often share characteristic compositional and functional patterns shaped by factors such as early microbial seeding, lifelong environmental exposures, and age-related physiological changes. Birth and early feeding establish the initial gut microbiome, with maternal transmission and milk-derived substrates typically favoring Bifidobacterium. As infants transition to solid foods and experience increasing social and environmental exposures, the microbiome undergoes substantial restructuring throughout childhood and adolescence. In adulthood, functional redundancy underpins stability despite routine perturbations; later life brings greater compositional uniqueness, with some profiles losing core taxa and accommodating opportunistic species, whereas others, particularly healthy older adults and centenarians, retain distinctive metabolic capacities that may buffer inflammaging. Efforts to build microbiome "aging clocks" highlight potential to index biological age, but progress remains constrained by technical and methodological limitations and is still maturing. This review synthesizes current evidence and identifies priorities for developing microbiome-informed, life-stage-tailored interventions.},
}

@article {pmid42157525,
year = {2026},
author = {Aware, C and Woods, C and Khodakivskyi, P and Dwivedi, AK and Zuckerman, A and Govindarajan, M and Ivanich, K and Yu, W and Cui, J and Gu, Z and Goun, E and Ericsson, AC and Zafonte, R and Balchandani, P and Lin, AL},
title = {Stroke-induced gut microbiome dysbiosis accelerates Alzheimer's disease progression.},
journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism},
volume = {},
number = {},
pages = {271678X261449017},
doi = {10.1177/0271678X261449017},
pmid = {42157525},
issn = {1559-7016},
abstract = {Stroke survivors face an elevated risk of developing Alzheimer's disease (AD), yet the biological mechanisms linking these conditions remain poorly defined. Here, we show that a stroke-induced gut microbiome is a key driver of AD-related pathology. Fecal microbiota transplantation (FMT) from stroke patients into young triple-transgenic Alzheimer's disease (3xTg-AD) mice accelerated tau phosphorylation, increased neuroinflammation, and disrupted metabolic homeostasis in both the brain and gut, compared with FMT from healthy donors. Mice receiving stroke-derived microbiota exhibited persistent, donor-specific dysbiosis and broad metabolic reprogramming involving redox balance, nucleotide metabolism, and energy pathways in cecal contents and brain tissue. These metabolic disturbances were accompanied by widespread and region-specific transcriptional changes revealed by single-cell spatial transcriptomics, including glial activation, impaired neuron-glia communication, and dysregulation of mitochondrial, amyloid-processing and inflammatory pathways across cortical and hippocampal regions. Collectively, these findings identify post-stroke gut dysbiosis as a mechanistic contributor to heightened neurodegenerative vulnerability and AD risk, highlighting the gut-brain axis as a potentially modifiable target for preventing post-stroke dementia.},
}

@article {pmid42157533,
year = {2026},
author = {Deriouich, M and Dompmartin, A and L'Orphelin, JM},
title = {Ultraviolet Radiations Impact on the Skin-Brain Axis: A Literature Review of our Current Knowledge.},
journal = {Photodermatology, photoimmunology & photomedicine},
volume = {42},
number = {3},
pages = {e70097},
doi = {10.1111/phpp.70097},
pmid = {42157533},
issn = {1600-0781},
mesh = {Humans ; *Ultraviolet Rays/adverse effects ; *Brain/radiation effects ; *Skin/radiation effects/immunology/metabolism ; Animals ; Microbiota/radiation effects ; },
abstract = {BACKGROUND: Sunlight is essential for vitamin D synthesis and contributes to mood regulation, but it is also a major risk factor for skin aging and carcinogenesis. While the cutaneous and immune effects of ultraviolet radiation are well documented, its potential impact on brain function remains poorly understood. This review aims to synthesize current evidence on the effects of ultraviolet exposure on the central nervous system, with a particular focus on photoimmunological mechanisms and skin-derived signaling pathways.

METHODS: We conducted a narrative review of experimental and clinical studies investigating the systemic and neurological consequences of UV exposure. Findings from photodermatology, immunology, neuroscience, and microbiome research were integrated to examine potential skin-brain interactions.

RESULTS: UV exposure induces systemic inflammatory responses and immunosuppression, alters the skin microbiome, and modulates circulating neuroactive mediators. These processes are associated with changes in neurotransmitter systems, neuroplasticity, and brain structure in both animal models and human studies. Emerging evidence supports the existence of indirect pathways linking UV-induced skin and immune responses to central nervous system function, including immune and microbiota-related mechanisms.

CONCLUSION: Collectively, available data suggest that UV radiation may influence brain function indirectly through interconnected skin, immune, and microbiota pathways. As interest in balanced and "healthy" sun exposure increases, further interdisciplinary research is needed to clarify the neurological consequences of UV exposure and to assess its potential implications in photodermatology and photomedicine.},
}

Humans
*Ultraviolet Rays/adverse effects
*Brain/radiation effects
*Skin/radiation effects/immunology/metabolism
Animals
Microbiota/radiation effects

@article {pmid42157753,
year = {2026},
author = {Xu, H and Xu, B and Wang, H and Tao, R and Chen, R and Cheng, Y and Zheng, Z and Sun, D and Li, X},
title = {Lifestyle Modulation of Xenobiotic Stress: Aerobic Exercise Attenuates Nanoplastic-Associated Neuroendocrine Dysfunction via a Gut-Ovary-Brain Continuum.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {10},
pages = {e71891},
doi = {10.1096/fj.202600941R},
pmid = {42157753},
issn = {1530-6860},
support = {2025ZY01039//Central Government Funds For Guiding Local Scientific and Technological Development/ ; SHPY2025010//Scientific Research Cultivation Project of the College of Life and Environmental Sciences, Wenzhou University/ ; 2024K076//Quzhou Municipal Bureau of Science and Technology/ ; },
mesh = {Animals ; Female ; Zebrafish ; *Physical Conditioning, Animal/physiology ; *Ovary/drug effects/metabolism ; *Brain/metabolism/drug effects ; *Neurosecretory Systems/drug effects/metabolism ; Oxidative Stress/drug effects ; *Xenobiotics/toxicity ; *Nanoparticles/toxicity ; },
abstract = {Xenobiotic stress can disrupt neuroendocrine function, yet whether a modifiable lifestyle factor can alter internal burden and downstream toxicity remains unclear. Here, adult female zebrafish were exposed to polystyrene nanoplastics (NPs; 80 nm; 1.0 mg/L) for 21 days, with or without moderate aerobic exercise (AE; 12 cm/s, 20 min/day). NPs exposure alone caused significant ovarian accumulation of particle-like structures (TEM), elevated oxidative stress, increased follicular apoptosis (TUNEL), and disrupted reproductive hormones (E2, FSH, LH). It also induced anxiety- and depression-like behaviors in novel tank and shoaling tests, accompanied by elevated cortisol and altered monoamine (NE, 5-HIAA) levels. In contrast, concurrent AE markedly attenuated these effects: it reduced ovarian particle burden, improved antioxidant enzyme activities (SOD, POD), restored ovarian histoarchitecture, and normalized endocrine and neuroendocrine measures. These changes were supported by partial recovery of ovarian (ESR1, cyp19a1a, AMH) and brain (BDNF, TPH2) transcript levels. Gut microbiome profiling revealed that AE counteracted NPs-associated dysbiosis, enriching beneficial taxa, including Akkermansia and Lachnospiraceae_NK4A136_group. Predictive functional inference and correlation analyses linked these microbial shifts to enhanced fatty acid and tryptophan metabolic potential, which correlated with neuroendocrine recovery. Together, these data support a working model in which AE acts as an exposure modifier, coupling host physiology and microbiome-associated metabolic capacity to mitigate NPs-induced neuroendocrine dysfunction via a gut-ovary-brain continuum. Targeted metabolomics and causal microbiota perturbation will be needed to validate specific mediators.},
}

Animals
Female
Zebrafish
*Physical Conditioning, Animal/physiology
*Ovary/drug effects/metabolism
*Brain/metabolism/drug effects
*Neurosecretory Systems/drug effects/metabolism
Oxidative Stress/drug effects
*Xenobiotics/toxicity
*Nanoparticles/toxicity

@article {pmid42157913,
year = {2025},
author = {Nawaz, Y and Munir, S and Aslam, S and Butt, FR and Tanvir, F and Nawaz, B and Bashir, K and Tahreem, R},
title = {The Bacterial Role in the Progression of Breast Cancer through Mechanism of Gene Action: Future Prospects with Existing Studies.},
journal = {Current genomics},
volume = {26},
number = {6},
pages = {458-468},
pmid = {42157913},
issn = {1389-2029},
abstract = {BACKGROUND: Breast cancer is the main cause of death for women, even with major improvements in treatment. Through processes like DNA damage, estrogen metabolism, and immunological regulation, bacterial populations have been shown to have an impact on breast cancer development in recent studies.

OBJECTIVES: This review aimed to examine and evaluate current research on the involvement of bacteria in breast cancer progression, with an emphasis on gene action mechanisms and potential future treatments targeting the microbiome.

METHODS: A thorough literature analysis was carried out to identify pertinent research published between 1989-2024 across various databases, including PubMed, Google Scholar, Google, and Scopus.

RESULTS: Bacterial dysbiosis in the gut and breast tissue contributes to the progression of breast cancer through different pathways. Double-strand breaks in DNA are linked to various bacteria, like Escherichia coli, Staphylococcus epidermidis, Helicobacter pylori, and Fusobacterium, which contribute to genomic instability. Breast cancers are influenced by hormones that are influenced by gut microbiota, namely the estrobolome, which regulates estrogen levels. Bacteria also impact immune responses by preventing anti-tumor immunity. These results suggest that restoring microbial balance to specific bacterial taxa may open up new treatment options. Different genes may contribute to variations, including an increase in regulatory T (Treg) cells, while FOXP3+ T cells are linked to shorter relapse-free survival. Understanding the microbiota's role in DNA damage, hormone regulation, and immune modulation is important.

CONCLUSION: Bacteria contribute significantly to the development of breast cancer through gene-level processes. Probiotics, immunomodulatory techniques, and microbiome-targeted treatments are potential future developments that could improve therapy effectiveness and reduce resistance.},
}

@article {pmid42157925,
year = {2026},
author = {Xiang, T and Xiao, S and Yang, C and Zhang, D and You, Y and Xie, L and Ling, Z and Wang, X and Zhang, C and Huang, G and Sun, D and Chen, Y and Luo, F},
title = {Tryptophan-Restricted Intermittent Diet Alleviates Estrogen Deficiency-Induced Osteoporosis via Regulating Coupling Effects of "Gut-Bone" Axis.},
journal = {International journal of biological sciences},
volume = {22},
number = {9},
pages = {4784-4805},
pmid = {42157925},
issn = {1449-2288},
mesh = {*Tryptophan ; Animals ; *Osteoporosis/metabolism/diet therapy/etiology ; *Gastrointestinal Microbiome/physiology ; Mice ; *Estrogens/deficiency ; Female ; Mice, Inbred C57BL ; *Bone and Bones/metabolism ; X-Ray Microtomography ; },
abstract = {Osteoporosis (OP) is a chronic and severe skeletal metabolic disorder resulting from excessive bone erosion activity and compromised bone formation. Emerging evidence highlights that the "gut-bone" axis plays a critical role in maintaining bone homeostasis via modulating gut microbiota and relevant metabolites. Individually, diet-derived tryptophan acts as one of the primary environmental factors that modulate the microbiota-bone crosstalk. Nevertheless, the promising modulatory mechanism of the "diet-microbiome-bone" axis remains unknown during OP progression. In this regard, the study focused on the dominant role of tryptophan-restricted intermittent diet during estrogen deficiency-induced OP. Upon these findings, micro-computed tomography (μCT) evaluation and histomorphometric analysis have confirmed that treatment with tryptophan-restricted intermittent diet effectively mitigated bone loss and improved bone microarchitecture. To unravel the underlying mechanism, we performed 16S rDNA gene sequencing and untargeted metabolomics to confirm the alteration of microbial community composition and metabolite profiles. Additionally, biotin was further identified as a significant microbiota-derived metabolite involved in M1 macrophage polarization and mature osteoclast apoptosis when administered with tryptophan-restricted intermittent diet. Thus, we summarized that treatment with tryptophan-restricted intermittent diet could perform a protective function during OP via modulating the coupling effects of gut microbiota and bone homeostasis, which may provide a potential therapeutic strategy for OP.},
}

*Tryptophan
Animals
*Osteoporosis/metabolism/diet therapy/etiology
*Gastrointestinal Microbiome/physiology
Mice
*Estrogens/deficiency
Female
Mice, Inbred C57BL
*Bone and Bones/metabolism
X-Ray Microtomography

@article {pmid42158361,
year = {2026},
author = {Louise Jespersen, M and Kjærgaard Munk, K and Fjermedal, S and Pilgaard, B and Meyer, AS and Aarestrup, FM and Otani, S},
title = {A Hadza-enriched Prevotella/Segatella xyloglucanase shows sequence conservation and functional specialization.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2673265},
pmid = {42158361},
issn = {2993-3935},
abstract = {Bacteria can adapt to their environment through changes in their genetic material. A large proportion of gut bacteria are shaped by host-specific diet, including complex carbohydrates. The bacterial abundance, genetic content within the same bacterial species, and sequence-level variation in genes encoding similar carbohydrate-processing enzymes may therefore vary across hosts with different diets. We previously found that the abundance of diet-degrading genes varies between hominid host populations from Tanzania. We therefore hypothesized that, in addition to these abundance differences, selective pressure could act on individual gene sequences. Here, we investigated Tanzanian hominid gut microbiome differences at the taxonomic, genetic, structural, and functional levels. We analyzed 15,146 metagenome-assembled genomes (MAGs) spanning 1563 species and identified one species with striking host-associated separation. In particular, sequence variation in a xyloglucanase-encoding gene correlated strongly with the host population. This gene was highly conserved in the Hadza population, suggesting a role in the processing of diet-associated polysaccharides. Sequence differences and structural modeling revealed amino acid substitutions near the catalytic site, and biochemical assays using xyloglucan showed that representative variants differed in activity under identical assay conditions. Collectively, our findings suggest that host lifestyle and diet contribute to population-associated sequence variation in genes encoding enzymes involved in degrading polysaccharides.},
}

@article {pmid42158390,
year = {2026},
author = {Zhang, J and Ren, Y and Jia, Y and Li, B and Chen, C and Hu, W and Jia, S and Li, D and Liu, Y},
title = {Effects of tangerine peel flavonoids on flavor compounds and microbial communities in cigar tobacco fermentation: insights from ion migration chromatography and microbiomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1793725},
pmid = {42158390},
issn = {1664-302X},
abstract = {INTRODUCTION: It is reported that addition of tangerine peel extract (flavonoids) can significantly improve the quality and flavor of tobacco leaves during fermentation. Nobiletin, tangeretin and hesperidin are the predominant flavonoids present in tangerine peel. However, their effects on the fermentation process of cigar tobacco leaves (CTL) have not yet been elucidated.

METHODS: Three major tangerine peel flavonoids, hesperidin (CPG), nobiletin (CCPS) and tangeretin (JPS), were applied during the fermentation of CTL) to evaluate their effects on fermentation outcomes. Gas chromatography-ion mobility spectrometry (GC-IMS) and microbiome analysis based on 16S rRNA and internal transcribed spacer sequencing were employed to characterize volatile flavor compounds and microbial community dynamics during the 30 days of fermentation.

RESULTS: A total of 157 volatile compounds were identified in CTL in this study. All tangerine peel flavonoid treatments improved the flavor quality of tobacco leaves by modulating the microbial community. The CPG group was enriched in esters and acids (e.g., n-amyl formate and propyl acetate), contributing to fruity aroma, with high relative abundances of Firmicutes and Staphylococcus, and a slight increase in Bacillus. The CCPS group accumulated abundant ketones (e.g., 3-methyl-2-cyclopenten-1-one, 3-pentanone, and 2-hydroxy-2-methyl-4-pentanone), providing caramel-like sweetness and enhancing the smoke body, while the enrichment of Sphingomonas, Rhizobium and other genera elevated bacterial diversity. The JPS group formed characteristic volatile compounds showed the highest fungal richness among all treatments. The mixed flavonoid (HHHT) group exhibited the highest abundance of Firmicutes and Staphylococcus, the lowest proportion of Proteobacteria, nearly undetectable harmful microorganisms, and the lowest microbial diversity. All treatment groups shared certain microbial trends, but distinct microbial profiles were observed among the CPG, CCPS, JPS, and HHHT groups, with significant correlations between key microorganisms and volatile flavor compounds.

DISCUSSION: In this study, the influence of tangerine peel flavonoids on CTL flavor quality and microbial community was systematically analyzed. These findings demonstrated that tangerine peel flavonoids enhanced flavor of CTL by modulating microbial communities during fermentation, and this provides new insights into CTL processing.},
}

@article {pmid42158396,
year = {2026},
author = {McIntyre, DB and Barton, PS and Preston, S and Long, BM},
title = {Microbial succession in decomposing carrion is driven by time, modulated by insects and microbial perturbation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1773208},
pmid = {42158396},
issn = {1664-302X},
abstract = {Recent research into decomposition has shed light on the intricate interplay within multi-kingdom communities, with microbial populations emerging as key players in the breakdown process and emphasizing their interactions within the broader decomposer ecosystem. Despite this, the specific roles and regulatory mechanisms of microbial communities remain underexplored. Gaining deeper insight into these dynamics is essential for advancing ecological and forensic sciences. This study examines the role of microbes in decomposition, particularly in relation to insect activity and external microbiome alterations. We used 12 piglet (Sus scrofa) cadavers placed in a rural area in southern Australia, to investigate how experimental insect exclusion and microbial perturbation affects decomposition. Bacterial microbial composition was quantified using 16S technology and compared among treatments and time points. Results showed significant shifts in bacterial diversity and abundance across time points sampled, with early-stage decomposition characterized by a higher abundance of Firmicutes and Actinobacteria, followed by a dominance of Proteobacteria in later stages. Principal coordinate analysis confirmed these patterns, showing that while decomposition stage is the primary driver of diversity, insect access and microbial perturbation shape microbial stability and community shifts rather than overall diversity. This challenges assumptions that external factors strongly influence diversity and highlights the need to consider both time and microbial dynamics in forensic applications, particularly for post-mortem interval estimation.},
}

@article {pmid42158523,
year = {2026},
author = {Muhammad, N},
title = {Nanobiotic-Enhanced Probiotics for Targeted Gut Delivery: Mechanisms, Therapeutic Applications, and Translational Challenges.},
journal = {International journal of nanomedicine},
volume = {21},
number = {},
pages = {607382},
pmid = {42158523},
issn = {1178-2013},
mesh = {*Probiotics/administration & dosage/therapeutic use ; Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Drug Delivery Systems/methods ; Gastrointestinal Tract/microbiology ; Gastrointestinal Diseases/therapy/microbiology ; Translational Research, Biomedical ; Nanotechnology ; Nanoparticles/chemistry ; },
abstract = {The gut microbiota plays a pivotal role in maintaining human health by influencing physiological processes such as digestion, immune regulation, and metabolism. However, disruptions in gut microbial balance, or dysbiosis, are associated with numerous disorders. Probiotics have emerged as potential therapeutic agents, but their efficacy is limited by challenges such as low survival during gastrointestinal transit, poor colonization, and lack of targeted delivery. Nanotechnology has recently provided promising solutions to these limitations by enhancing the stability, viability, and functionality of probiotics. To provide an updated perspective, this article presents a structured narrative review informed by a PRISMA-guided literature search and screening process. Relevant studies published between 2021 and 2025 were identified from PubMed, Scopus, IEEE Xplore, and Google Scholar and were narratively synthesized to examine nanoencapsulation strategies, hybrid nanobiotic systems, smart delivery platforms, therapeutic applications, and translational barriers. Nanoencapsulation techniques, hybrid nanobiotic systems, and smart delivery platforms are at the forefront of probiotic enhancement. These systems improve protection of probiotics against harsh gastric conditions and enable targeted release within specific regions of the gastrointestinal tract, thereby enhancing colonization efficiency and therapeutic potential. Moreover, nanobiotics show promise in modulating gut microbiota composition, strengthening immune responses, and opening new therapeutic avenues for the management of gastrointestinal disorders, metabolic diseases, and immune-related conditions. Despite these advances, challenges related to safety, scalability, and regulatory approval remain significant barriers to clinical translation. This review synthesizes recent progress in nanobiotic-enhanced probiotics, evaluates their therapeutic applications, and discusses key challenges and future directions for precision microbiome therapeutics.},
}

*Probiotics/administration & dosage/therapeutic use
Humans
*Gastrointestinal Microbiome/drug effects
Animals
*Drug Delivery Systems/methods
Gastrointestinal Tract/microbiology
Gastrointestinal Diseases/therapy/microbiology
Translational Research, Biomedical
Nanotechnology
Nanoparticles/chemistry

@article {pmid42158622,
year = {2026},
author = {Math, RK and Javaregowda, PK and Patil, SG},
title = {Effect of Yoga and Meditation on Human Gut Microbiota: A Systematic Review.},
journal = {International journal of yoga},
volume = {19},
number = {1},
pages = {41-53},
pmid = {42158622},
issn = {0973-6131},
abstract = {The evidence from the clinical studies on the influence of yoga and meditation on gut microbiota in humans has been summarized in this systematic review. Searches were conducted until November 2023 in four electronic databases: SCOPUS, PubMed, Google Scholar, and Cochrane Controlled Registry of Trials (CENTRAL) to find relevant studies published in English. Studies on the influence of yoga and meditation on gut microbiome in human participants of any age or gender were included in the systematic review. The outcomes were modulations in the composition and function of gut microbiota and their metabolite levels. Due to the varied approaches used in the study designs and outcome measures of the included studies, a narrative synthesis was carried out. The database search resulted in 247 titles and abstracts, out of which four articles were included for qualitative synthesis. There was one nonrandomized controlled study and three observational studies. The studies were conducted on a healthy population (n = 440). The participants were followers of a vegan or vegetarian diet. The control group subjects were nonmeditators, i.e., who never received any meditation training. All the reviewed studies have shown a favorable change in the composition and function of gut microbiota and their metabolites with meditation practice when compared to controls. Yoga and meditation improved the composition and function of gut microbiota. However, all the subjects were following a vegetarian/vegan diet, so the beneficial changes demonstrated in the gut microbiota may be attributed to the combined effects of meditation and a vegetarian/vegan diet.},
}

@article {pmid42158814,
year = {2026},
author = {Wu, CK and Cheng, IS and Chung, YC and Liu, MF and Lin, YK and Lin, YH and Morris, K and Chang, D and Chiang, CF and Yang, MT},
title = {The Effects of a Prebiotic Formula Promoting Akkermansia muciniphila (AKK) on Gut Health: A Single-Centre, Randomised Controlled Trial.},
journal = {International journal of medical sciences},
volume = {23},
number = {6},
pages = {1952-1965},
pmid = {42158814},
issn = {1449-1907},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Prebiotics/administration & dosage ; Male ; Female ; Adult ; Middle Aged ; Verrucomicrobia ; Feces/microbiology ; Akkermansia ; },
abstract = {BACKGROUND: Gut health is closely associated with metabolic homeostasis, and alterations in gut microbiota composition have been linked to inflammation and metabolic disorders. Prebiotics targeting specific taxa, such as Akkermansia muciniphila, have attracted interest for their potential to modulate gut microbiota composition. While preclinical studies have suggested a role for A. muciniphila in gut-related metabolic pathways, clinical evidence supporting its effects on microbiome regulation and metabolic outcomes remains limited. Therefore, this study aimed to explore the effects of a prebiotic blend designed to promote A. muciniphila on gut microbiota composition and selected physiological parameters.

METHODS: Seventy participants were randomized to receive either placebo or the AKK formula for 8 weeks. Anthropometric assessments, blood tests, and stool examinations were performed at baseline and at weeks 4 and 8. The main analyses were conducted in the per-protocol population (n = 25 per group).

RESULTS: The results revealed no significant markers of liver or kidney dysfunction in either group. The AKK formula group showed an increased qPCR-derived relative abundance of A. muciniphila compared with total bacteria. Gut microbiome analysis further demonstrated selective changes in gut microbiota composition in the AKK formula group, including an increased relative abundance of Bifidobacterium and decreased relative abundances of Proteobacteria, Erysipelotrichia, and Escherichia-Shigella. A trend toward lower gastrointestinal discomfort scores was observed in the AKK formula group during the intervention period.

CONCLUSIONS: The AKK formula increased the relative abundance of A. muciniphila, was associated with selective modulation of gut microbiota composition, and showed a trend toward reduced gastrointestinal discomfort, supporting its potential relevance in future gut health research.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Prebiotics/administration & dosage
Male
Female
Adult
Middle Aged
Verrucomicrobia
Feces/microbiology
Akkermansia

@article {pmid42158827,
year = {2026},
author = {Lin, LT and Li, CJ and Lin, PH and Cheng, SH and Raj, EN and Chen, YC and Chern, CU and Wen, ZH and Tsui, KH},
title = {Targeted Vaginal Microbiome Modulation by Postbiotic Intervention Reduces Dysbiosis-Associated Pathogens in Infertile Women: A Pilot Study.},
journal = {International journal of medical sciences},
volume = {23},
number = {6},
pages = {1921-1932},
pmid = {42158827},
issn = {1449-1907},
mesh = {Humans ; Female ; *Dysbiosis/microbiology/drug therapy/therapy ; Adult ; *Vagina/microbiology/drug effects ; Pilot Projects ; *Microbiota/drug effects/genetics ; Pregnancy ; *Infertility, Female/microbiology/therapy ; Embryo Transfer/methods ; Lactobacillus/drug effects/isolation & purification/genetics ; Fertilization in Vitro/methods ; RNA, Ribosomal, 16S/genetics ; Pregnancy Rate ; *Antimicrobial Peptides/administration & dosage ; },
abstract = {BACKGROUND: Vaginal dysbiosis characterized by depleted Lactobacillus populations is associated with impaired fertility outcomes in women undergoing assisted reproduction. Postbiotic interventions delivering antimicrobial peptides without live bacteria may offer targeted microecological modulation while preserving community stability. We investigated the microbial and clinical effects of an eight-week antimicrobial peptide-based postbiotic in infertile women.

METHODS: Fifteen infertile women (mean age 38.7 ± 4.1 years) with ≥ 2 prior in vitro fertilization failures received intravaginal postbiotic therapy (VAGINNE[®], Good-Care Biotech, Ltd.) for 8.0 ± 0.3 weeks before frozen embryo transfer (FET). Paired vaginal samples collected pre- and post-treatment underwent full-length 16S rRNA gene sequencing using PacBio Sequel platform. Microbiome composition, beta-diversity, differential abundance, and absolute bacterial load were analyzed.

RESULTS: The cohort achieved a clinical pregnancy rate of 46.7% (7/15) following postbiotic intervention and subsequent FET. Beta-diversity analysis revealed preservation of global community structure (PERMANOVA R² = 0.05, p = 0.65), indicating ecological stability. Despite cohort-level stability, patient-specific analysis identified favorable microbiome restructuring in 73% of participants (11/15), including emergence of Lactobacillus-dominant communities in previously dysbiotic profiles. Absolute abundance quantification demonstrated selective elimination of dysbiosis-associated pathogens: Prevotella decreased from 408.47±990.78 to 0.29±0.83 cells/sample (p < 0.01), Pseudomonas from 419.07±567.04 to 89.14±114.42 (p < 0.05), and complete clearance of Howardella (3.53±9.87 to undetectable). Conversely, Gluconacetobacter increased significantly from undetectable to 2.93±4.18 cells/sample (p < 0.05).

CONCLUSIONS: In this pilot cohort, antimicrobial peptide-based postbiotic therapy was associated with encouraging pregnancy outcomes and targeted pathogen clearance. The intervention selectively reduced high-burden detrimental taxa while maintaining microbiome architectural integrity, supporting precision microecological modulation as a promising adjuvant strategy for reproductive health.},
}

Humans
Female
*Dysbiosis/microbiology/drug therapy/therapy
Adult
*Vagina/microbiology/drug effects
Pilot Projects
*Microbiota/drug effects/genetics
Pregnancy
*Infertility, Female/microbiology/therapy
Embryo Transfer/methods
Lactobacillus/drug effects/isolation & purification/genetics
Fertilization in Vitro/methods
RNA, Ribosomal, 16S/genetics
Pregnancy Rate
*Antimicrobial Peptides/administration & dosage

@article {pmid42158829,
year = {2026},
author = {Zhao, ZK and Ma, JL and Lu, F and Wang, SJ},
title = {Exosomes in Inflammatory Bowel Disease: Mechanisms, Diagnostic Potential, and Engineering Strategies for Precision Therapy.},
journal = {International journal of medical sciences},
volume = {23},
number = {6},
pages = {2141-2153},
pmid = {42158829},
issn = {1449-1907},
mesh = {*Exosomes/metabolism/immunology ; Humans ; *Inflammatory Bowel Diseases/diagnosis/therapy/immunology ; Biomarkers/metabolism ; *Precision Medicine/methods ; Gastrointestinal Microbiome/immunology ; Drug Delivery Systems/methods ; Animals ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic gastrointestinal disorder characterized by immune dysregulation, epithelial barrier dysfunction, and microbial imbalance. Despite progress in biologic therapies, challenges such as variable efficacy, systemic side effects, and the lack of reliable biomarkers remain significant obstacles in clinical management. Exosomes, key mediators of intercellular communication, play a pivotal role in IBD's pathogenesis by transporting bioactive substances. Increasing evidence links exosomes to critical IBD processes, including Th17/Treg imbalance, inflammasome activation, and host-microbiome interactions. Exosomes also show potential as minimally invasive biomarkers for disease activity and subtype differentiation. Furthermore, advancements in exosome engineering, including surface modification and hybrid nanostructure development, enhance their potential for targeted drug delivery and immune modulation in IBD. This review summarizes the role of exosomes in IBD, their diagnostic potential, and emerging exosome-based therapeutic strategies.},
}

*Exosomes/metabolism/immunology
Humans
*Inflammatory Bowel Diseases/diagnosis/therapy/immunology
Biomarkers/metabolism
*Precision Medicine/methods
Gastrointestinal Microbiome/immunology
Drug Delivery Systems/methods
Animals

@article {pmid42159017,
year = {2026},
author = {Baumann, PC and Pospich, R and Döhner, K and Klug, I and Guerrero, JCV and Hartmann, J and Harder, I and Lieb, W and Kind, B and Kleinheinz, A and Abraham, S and Augustin, M and Weisshaar, E and Schmitt, J and Weidinger, S and Sodeik, B and Werfel, T and Roesner, LM and Traidl, S and , },
title = {Keratinocyte Priming by Staphylococcus aureus Reduces HSV-1 Susceptibility.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70392},
pmid = {42159017},
issn = {1398-9995},
abstract = {BACKGROUND: Individuals with atopic dermatitis (AD) are at increased risk for skin infections, including eczema herpeticum (EH), a severe condition caused by herpes simplex virus type 1 (HSV-1). While AD skin is often colonized by Staphylococcus aureus (S. aureus), its role in EH susceptibility remains unclear. Here we aim to investigate differences in the skin microbiome of AD patients with (ADEH[+]) and without (ADEH[-]) EH and examine the impact of S. aureus and S. epidermidis on HSV-1 infection in an in vitro keratinocyte model.

METHODS: 16S microbiome sequencing was performed on skin samples from ADEH[+], ADEH[-], and healthy controls. To investigate microbial effects on HSV-1 infection, keratinocytes were pre-incubated with heat-killed S. aureus (HKSA) or S. epidermidis (HKSE), followed by HSV-1 infection in the presence or absence of the Th2 cytokines IL-4 and IL-13, simulating the conditions of AD lesional skin. Infection rates and transcriptomic changes were analyzed.

RESULTS: ADEH[+] patients showed a reduced microbial diversity compared to ADEH[-], with increased S. aureus and S. epidermidis colonization. HKSA, but not HKSE, protected keratinocytes from HSV-1 infection and reduced the release of infectious progeny virus. Transcriptome analysis of keratinocytes revealed HKSA-induced upregulation of interferon pathways and antimicrobial peptides, and downregulation of HSV-1 entry factors.

CONCLUSION: Pre-incubation with S. aureus set basal keratinocytes into an alarmed state, restricting HSV-1 infection presumably via downregulation of receptors important for viral entry and activation of antiviral pathways.},
}

@article {pmid42159080,
year = {2026},
author = {Junaid, M and Zeming, H and Zhu, Y},
title = {The Leptin Renaissance: Orchestrating the Next Endocrine Paradigm.},
journal = {Journal of cellular biochemistry},
volume = {127},
number = {5},
pages = {e70091},
doi = {10.1002/jcb.70091},
pmid = {42159080},
issn = {1097-4644},
support = {2024Z034//Major Project of 2035 Sci & Tech Innovation of Ningbo/ ; 2024Z204//Major Project of 2035 Sci & Tech Innovation of Ningbo/ ; //K.C. Wang Magna/Education Fund of Ningbo University/ ; },
mesh = {*Leptin/metabolism/immunology ; Humans ; Animals ; *Obesity/metabolism/immunology ; *Gastrointestinal Microbiome ; Energy Metabolism ; Endocrine System/metabolism ; Signal Transduction ; Homeostasis ; },
abstract = {Leptin, a hormone historically recognized for regulating appetite and energy homeostasis, is increasingly appreciated as a central mediator of immune function, metabolic integration, and tissue-specific signaling. Despite decades of research, leptin resistance limits the efficacy of conventional therapies, such as hormone replacement, in treating obesity and related disorders. Emerging evidence demonstrates that leptin interacts bidirectionally with the gut microbiome, influencing systemic metabolism and immune responses. Advances in multi-omics profiling, synthetic biology, and tissue-targeted therapeutics provide unprecedented opportunities to overcome these barriers. Here, we present a perspective emphasizing integrative strategies that combine precision medicine, immune modulation, engineered leptin analogs, and microbiome-targeted interventions. Leveraging these innovations could redefine leptin-based therapies, enabling system-level restoration of metabolic and immune homeostasis. Understanding leptin as a pleiotropic, multi-system hormone positions it at the forefront of the next endocrine paradigm.},
}

*Leptin/metabolism/immunology
Humans
Animals
*Obesity/metabolism/immunology
*Gastrointestinal Microbiome
Energy Metabolism
Endocrine System/metabolism
Signal Transduction
Homeostasis

@article {pmid42159306,
year = {2026},
author = {Sakai, M and Mori, I and Kawasaki, A and Takigawa, H and Kinoshita, K and Aosaki, T and Sakasai, M and Sugai, Y},
title = {Kytococcal and Staphylococcal strains isolated from Japanese subjects with foot malodor and their control.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag121},
pmid = {42159306},
issn = {1365-2672},
abstract = {AIMS: Human foot malodor has been reported to be derived from volatile fatty acids, mainly isovaleric acid, generated by foot bacteria, especially staphylococcal species. However, the knowledge of foot odor is limited compared with axillary odor. Therefore, this study was conducted to identify the causative bacteria of foot malodor in Japanese individuals and to explore methods for controlling foot odor.

METHODS AND RESULTS: 16S rRNA gene-targeted microbiome analysis and qPCR analysis were performed on samples from the plantar surface and toe clefts. 16S rRNA gene sequencing was used to identify isolates. Commercially available botanical extracts were screened for their ability to inhibit microbial production of malodorous compounds, specifically the conversion of L-leucine to isovaleric acid. Microbiome analysis and qPCR indicated that Kytococcus is associated with the intensity of isovaleric acid-like odor. 16S rRNA gene analysis of isolates identified Kytococcus schroeteri and Staphylococcus hominis as isovaleric acid-producing strains. Screening of botanical extracts revealed that Sanguisorba officinalis and Eucalyptus globulus extracts effectively inhibited the generation of isovaleric acid from L-leucine.

CONCLUSIONS: Kytococcus, particularly K. schroeteri and S. hominis are implicated in isovaleric acid-mediated foot malodor in Japanese subjects. Extracts of Sanguisorba officinalis and Eucalyptus globulus show potential as control agents by inhibiting microbial production of isovaleric acid.},
}

@article {pmid42159380,
year = {2026},
author = {Shao, H and Yoo, H and Cai, J-N and Jung, H-Y and Kang, C-M and Jeon, J-G and Kim, D},
title = {H2O2-producing commensal streptococci disrupt Streptococcus mutans-Candida albicans synergism.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0033326},
doi = {10.1128/aem.00333-26},
pmid = {42159380},
issn = {1098-5336},
abstract = {Microbial homeostasis is maintained by the antagonistic capacity of commensal bacteria against cariogenic pathogens. In the oral cavity, commensal Streptococcus, dominant colonizers of the tooth surface, can produce hydrogen peroxide (H2O2), modulating virulent cross-kingdom biofilm formation. To investigate their ecological role, clinical isolates from dental plaque were compared with reference strains, including Streptococcus oralis ATCC 35037 and S. oralis subsp. tigurinus J22 to determine their H2O2-producing capabilities. The antagonistic potential of S. oralis against Streptococcus mutans and Candida albicans was evaluated using microbial and biochemical assessments. In a saliva-coated hydroxyapatite disc model, S. oralis strains were co-cultured with S. mutans and C. albicans. A high H2O2-producing S. oralis J22 inhibited EPS formation in S. mutans and yeast-to-hypha transition in C. albicans, thereby reducing EPS-mediated bacterial-fungal cell colocalization. Time-lapse confocal imaging revealed that S. oralis J22 dominated the biofilm through H2O2-mediated antagonistic interactions. In contrast, the inhibitory effect of S. oralis strains lacking the spxB gene on cross-kingdom biofilms was significantly reduced. These data provide ecological insights into how physicochemical properties of early colonizing commensals shape the structure and virulence of cross-kingdom oral biofilm through antimicrobial-mediated antagonistic activity.IMPORTANCEThe co-existence of S. mutans and C. albicans accelerates the development of severe early childhood caries, particularly under frequent sucrose exposure. This study demonstrates that early colonizing and antimicrobial-producing oral commensal bacteria can disrupt these pathogenic interactions by modulating their physicochemical associations. These findings highlight the potential of enhancing commensal bacteria as part of novel caries prevention strategies. Further characterization of the functional oral microbiota, especially clinically relevant oral commensals, could advance the development of diagnostic biomarkers and microbiome-targeted therapeutics to prevent painful and costly oral diseases.},
}

@article {pmid42159387,
year = {2026},
author = {Wang, X-R},
title = {mSphere of Influence: How a gut microbiota study reshaped my thinking on tick-borne pathogens.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0021326},
doi = {10.1128/msphere.00213-26},
pmid = {42159387},
issn = {2379-5042},
abstract = {Xin-Ru Wang works in tick biology and intracellular bacterial pathogenesis. In this mSphere of Influence article, she reflects on how "Gut microbiota of the tick vector Ixodes scapularis modulate colonization of the Lyme disease spirochete" by Narasimhan et al. (2014) reshaped her understanding of vector competence by placing pathogen colonization within the ecological context of the tick microbiome. Her laboratory studies Rickettsia-tick cell interactions, including autophagy, apoptosis, and innate immune signaling. Here, she examines how this ecological framework extends to the intracellular level, where pathogenic Rickettsia may encounter cellular environments already shaped by resident endosymbionts.},
}

@article {pmid42159410,
year = {2026},
author = {Rodriguez, TN and Smeyne, RJ and Smeyne, M},
title = {Neurobiology of exercise in Parkinson's disease.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261452869},
doi = {10.1177/1877718X261452869},
pmid = {42159410},
issn = {1877-718X},
abstract = {Epidemiological, preclinical, and clinical studies increasingly support exercise as a potent neuroprotective and disease-modifying intervention in Parkinson's disease (PD). Preclinical studies, including toxin- and α-synuclein-based models, using voluntary, forced, and skilled exercise paradigms demonstrate preservation of nigrostriatal dopaminergic neurons, improved motor function, and activation of convergent pathways. Protective processes include upregulation of neurotrophic factors (BDNF, GDNF, VEGF and Irisin), enhanced mitochondrial biogenesis and oxidative resilience, reduced neuroinflammation, improved basal ganglia synaptic plasticity and increased lysosomal functions. Additional emerging mechanisms underlying exercise-induced neuroprotection involve vascular remodeling, pathways regulating cellular oxygen and hypoxia, modulation of the gut microbiome, and epigenetic reprogramming. Importantly, clinical studies mirror these preclinical findings, demonstrating improvements in motor symptoms, balance, fitness, and quality of life, along with functionally positive changes in exercise-responsive biomarkers such as BDNF, irisin, and glutathione. Collectively, these highlight exercise as a robust, multifaceted therapeutic strategy with significant implications for PD prevention and management. This review synthesizes findings from the past 5 years across preclinical models and patient studies to define how exercise reduces PD risk, slows symptom progression, and engages biological pathways relevant to neuroprotection and restoration.Lay abstractExercise, as a consistent lifestyle habit, is beneficial to overall health with cardiovascular and cognitive benefits; and also supports a better quality of life throughout aging. Exercise has been demonstrated to reduce the risk of developing Parkinsons's Disease as well as to delay the symptoms of PD. In this review we will report recent (2020-2025) preclinical and clinical studies that examine the mechanisms underlying exercise's neuroprotective benefit related to PD.},
}

@article {pmid42159601,
year = {2026},
author = {Yang, Y and Lian, S and Li, X and Tang, Y and Su, Y and Zhang, Z and Li, M and Guo, Y and He, Z and Shen, Y},
title = {Unveiling metagenomic and metabolomic signatures in mild and severe pneumonia caused by Mycoplasma pneumoniae in children.},
journal = {Microbial genomics},
volume = {12},
number = {5},
pages = {},
pmid = {42159601},
issn = {2057-5858},
mesh = {Humans ; *Mycoplasma pneumoniae/genetics/pathogenicity/metabolism ; *Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis ; Female ; Male ; Child, Preschool ; Child ; *Metagenomics/methods ; *Metabolomics/methods ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; Infant ; Severity of Illness Index ; Microbiota ; Machine Learning ; Anti-Bacterial Agents/pharmacology ; },
abstract = {Background. Mycoplasma pneumoniae (MP) is a common causative pathogen of community-acquired pneumonia in children, with clinical presentations ranging in severity. Early stratification and timely intervention are essential for improving patient outcomes. However, a major clinical challenge lies in the limited ability to accurately distinguish between mild and severe cases based solely on early clinical indicators.Methods. This prospective real-world study investigated the differences in microbiome and metabolomics between mild and severe MP pneumonia (MPP) in children. Bronchoalveolar lavage fluid samples were collected from 153 children and subjected to metagenomic sequencing and non-targeted metabolomic analysis. Meanwhile, to enhance early diagnostic accuracy, this study developed a machine learning classification model and validated it using a third-party validation set.Results. The results revealed significant alterations in the abundance of specific bacterial communities in the severe group, most notably the coexistence of MP and Alphainfluenzavirus influenzae, which may contribute to disease exacerbation through synergistic pathogenic mechanisms. Furthermore, the macrolide resistant rate of MP in the severe group exceeded 80%, emphasizing the importance of appropriate antibiotic selection. Metabolomic analysis showed a significant enrichment of metabolites related to cellular energy metabolism and immune regulation in severe cases. The model demonstrated exceptional predictive performance, achieving an area under the curve ranging from 0.909 to 0.991, which significantly outperformed conventional clinical stratification methods.Conclusions. These findings elucidate the distinct pathophysiological mechanisms underlying both mild and severe MP infections and provide a promising framework for improving early diagnosis and personalized treatment strategies in paediatric MPP.},
}

Humans
*Mycoplasma pneumoniae/genetics/pathogenicity/metabolism
*Pneumonia, Mycoplasma/microbiology/metabolism/diagnosis
Female
Male
Child, Preschool
Child
*Metagenomics/methods
*Metabolomics/methods
Prospective Studies
Bronchoalveolar Lavage Fluid/microbiology
Infant
Severity of Illness Index
Microbiota
Machine Learning
Anti-Bacterial Agents/pharmacology

@article {pmid42159807,
year = {2026},
author = {Fulaneti, FS and Brasil-Neto, ES and Rumpel, VS and de Paula Ribeiro, L and Brum, LN and Cipriani, LP and Martin, TN},
title = {Microbial co-inoculation and extracellular vesicles: new frontiers for soybean productivity.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42159807},
issn = {1572-9699},
mesh = {*Glycine max/microbiology/growth & development ; *Extracellular Vesicles/metabolism ; Bacteria/metabolism/genetics ; Soil Microbiology ; Crops, Agricultural/growth & development/microbiology ; Agriculture/methods ; *Agricultural Inoculants ; },
abstract = {Over the past decades, the intensive use of chemical fertilizers in agriculture has shown low efficiency while causing serious environmental issues and leading to soil nutrient imbalances. These challenges are compounded by climate change, increasing incidence of diseases and pests, and soil acidification, factors that jeopardize agricultural productivity and, consequently, threaten global food security. Soybean (Glycine max L.) is one of the world's most important crops, serving as a key source of protein and oil for both human consumption and animal feed. Its global relevance continues to grow with rising demand for food, biofuels, and industrial applications, with Brazil, the United States, and Argentina leading production. Beyond its economic value, soybean contributes to agricultural sustainability through symbiotic nitrogen fixation, reducing the need for synthetic fertilizers. However, maintaining high yields under changing environmental conditions requires innovative management strategies. In this context, one promising strategy to mitigate these problems is the use of plant growth-promoting bacteria (PGPB), which contribute to more sustainable crop yield. Although numerous studies are underway regarding the potential of PGPB, further research is still necessary due to the limited understanding of their mechanisms of action and the vast range of benefits they may offer. Currently, there is a wide variety of inoculants based on different bacterial species, which play a key role in stimulating plant growth and reducing reliance on agrochemicals. Among emerging technologies, noteworthy examples include molecular inoculants (still not widely adopted commercially), bacterial and fungal consortia formulated into a single product, and inoculants containing genetically edited microorganisms-all of which have shown great promise in enhancing the performance of beneficial microbial species. The selection and genetic editing of rhizosphere-associated PGPB-an essential component of the plant microbiome-are viable alternatives for promoting more sustainable agriculture. Thus, this review examines the main inoculant technologies aimed at obtaining efficient microorganisms capable of improving rhizosphere conditions and microbial community dynamics, representing a strategic opportunity for developing solutions that enhance soybean sustainability.},
}

*Glycine max/microbiology/growth & development
*Extracellular Vesicles/metabolism
Bacteria/metabolism/genetics
Soil Microbiology
Crops, Agricultural/growth & development/microbiology
Agriculture/methods
*Agricultural Inoculants

@article {pmid42159891,
year = {2026},
author = {McKay, S and Li, XM},
title = {Understanding Infantile Atopic Dermatitis: A Review of Environmental, Familial, Genetic and Microbial Influences.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42159891},
issn = {1534-6315},
mesh = {Humans ; *Dermatitis, Atopic/etiology/genetics/microbiology/epidemiology/prevention & control ; Infant ; Female ; Pregnancy ; Microbiota ; Infant, Newborn ; *Environmental Exposure/adverse effects ; Probiotics ; Risk Factors ; Gastrointestinal Microbiome ; },
abstract = {PURPOSE OF REVIEW: This review aims to clarify the early-life risk and protective factors associated with Infantile Atopic Dermatitis (IAD)-an inflammatory skin condition that typically develops between birth and two years of age. The goal was to examine recent findings on maternal, environmental, and microbial influences on IAD.

RECENT FINDINGS: Prenatal and postpartum maternal probiotic use may reduce IAD risk, though no significant alterations in infants' gut microbiota were found. Infants with IAD exhibit higher Clostridia levels, while Verrucomicrobia are more abundant in non-IAD cases. Breastmilk from the mother of affected infants contains higher arachidonic acid and lower eicosapentaenoic acid, whereas formula-feeding may lower IAD risk. Seasonal influences such as reduced sunlight or humidity are associated with higher susceptibility. Elevated skin biomarkers, including TARC/CCL17 and IL-8, have been observed in infants who later develop IAD. Early antibiotic exposure, particularly during the first trimester, also increases risk.  IAD is multifactorial, involving genetics, environment, and skin barrier dysfunction. Understanding the interplay between the microbiome, maternal influences, and environmental exposures may guide future preventive approaches. Further research into non-pharmacologic and microbiome-targeted interventions is warranted to delay or prevent IAD onset.},
}

Humans
*Dermatitis, Atopic/etiology/genetics/microbiology/epidemiology/prevention & control
Infant
Female
Pregnancy
Microbiota
Infant, Newborn
*Environmental Exposure/adverse effects
Probiotics
Risk Factors
Gastrointestinal Microbiome

@article {pmid42160091,
year = {2026},
author = {Ruiz-Torres, NG and Martínez-Sánchez, S and de León-Lorenzana, A and Mercado-Juárez, RA and Salloum, PM and Poulin, R and Gaona, O and Falcón, LI and Rico-Chávez, O},
title = {Drivers of Microbiome Composition Among Helminth Parasites Sharing the Same Insectivorous Bat Host.},
journal = {Molecular ecology},
volume = {35},
number = {10},
pages = {e70389},
doi = {10.1111/mec.70389},
pmid = {42160091},
issn = {1365-294X},
support = {BV200421//PAPIIT-DGAPA, UNAM/ ; IN218020//PAPIIT-DGAPA, UNAM/ ; },
mesh = {Animals ; *Chiroptera/parasitology/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota/genetics ; *Helminths/genetics/microbiology/classification ; Trematoda/microbiology/genetics ; Host-Parasite Interactions ; },
abstract = {Parasitic metazoans are increasingly recognised to form close associations with microbial taxa. Under the holobiont concept, these associations are an eco-evolutionary unit under joint selection. However, for most parasitic helminth species and particularly those associated with wildlife, these interactions and their effect on parasite evolution remain unknown. Investigating the factors determining the composition of helminth microbiomes is the first step towards a better understanding of helminth holobionts. Using the insectivorous bat Peropteryx kappleri and its parasitic helminths as a model system, we characterised the microbiome of 41 helminth individuals of four trematode and one nematode species in various bat intestinal and biliary microhabitats, along with bat tissues and luminal fluids. Our results based on 16S rRNA metabarcoding revealed that the microbiome composition of the different helminth species is partly influenced by their microhabitat (bat tissue), but ultimately each helminth species exhibits a distinctive microbial signature. Microbiome composition among the four trematode species showed no phylogenetic signal (no correlation with genetic similarity). Compared to the bat host, each helminth species exhibited enriched microbial taxa with putative symbiotic potential, some of which are commonly found in arthropods (potential intermediate hosts of helminths) and may be conserved throughout the parasite's life cycle. We propose that helminth microbiomes are determined by ecologically relevant factors and provide a basis for future functional research with implications for parasite establishment, development, and transmission.},
}

Animals
*Chiroptera/parasitology/microbiology
RNA, Ribosomal, 16S/genetics
Phylogeny
*Microbiota/genetics
*Helminths/genetics/microbiology/classification
Trematoda/microbiology/genetics
Host-Parasite Interactions

@article {pmid42160107,
year = {2026},
author = {Yan, G and Wang, S and Li, D and Liu, R and Zhang, Z and Zhang, Z and Kan, Y},
title = {Effects of dietary royal jelly supplementation on development, fecundity, and gut microbial community in Sarcophaga peregrina (Diptera: Sarcophagidae).},
journal = {Journal of economic entomology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jee/toag074},
pmid = {42160107},
issn = {1938-291X},
support = {231111111000//Key Research Project of Henan Province/ ; 251111113200//Key Research Project of Henan Province/ ; },
abstract = {Intensive laboratory rearing often reduces key phenotypic traits in farmed insects. We tested royal jelly (RJ) as a nutritional intervention in Sarcophaga peregrina (Robineau-Desvoidy) (Diptera: Sarcophagidae), assessing life-history traits and gut microbiota. Larvae were supplemented with RJ at 0%, 1%, 5%, or 10% (w/w, of the total bovine liver paste diet); a subset of emerging adults continued to receive the same RJ dose, creating "larval-only" and "larval + adult" dietary regimens. Although RJ did not alter mean larval weight at dispersal, it significantly accelerated larval growth and increased pupation rate. Adult lifespan was extended by larval supplementation and further prolonged when RJ was provided to both larvae and adults. Fecundity followed the same pattern: the "larval + adult" regimen exceeded the corresponding "larval-only" dose across concentrations. Dose-response relationships were non-linear, with modest gains at 1% and a plateau between 5% and 10%, indicating a mid-range optimum. 16S rRNA gene sequencing showed that RJ reduced gut α-diversity and shifted community composition; control-enriched taxa were suppressed under RJ. Functional predictions indicated that RJ-treated larvae harbored a gut microbiota with reduced metabolic potential, suggesting less microbial nutrient use and a lower immune challenge to the host. Together, results suggest that RJ is a promising tool to improve mass-rearing efficiency. Under our experimental conditions, a 5% RJ diet applied at both larval and adult stages appears to be an effective starting formulation, with the observed gains likely reflecting both direct nutritional benefits and microbiome restructuring.},
}

@article {pmid42160337,
year = {2026},
author = {Cabirol, A and Quinn, A and Schafer, J and Neuschwander, N and Kesner, L and Liberti, J and Engel, P},
title = {A defined community of core gut microbiota members promotes cognitive performance in honey bees.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {21},
pages = {e2608600123},
doi = {10.1073/pnas.2608600123},
pmid = {42160337},
issn = {1091-6490},
support = {892574//European Commission (EC)/ ; 714804//European Commission (EC)/ ; 219829/SNSF_/Swiss National Science Foundation/Switzerland ; 180575/SNSF_/Swiss National Science Foundation/Switzerland ; },
mesh = {Animals ; Bees/microbiology/physiology ; *Gastrointestinal Microbiome/physiology ; *Cognition/physiology ; Memory, Short-Term/physiology ; Germ-Free Life ; Bacteria/classification ; },
abstract = {Gut microbiota across animals have been shown to influence host cognition and behavior. However, it remains unclear whether these cognitive effects are driven by specific bacterial species or arise from community-level interactions. Here, we leveraged the honey bee (Apis mellifera) as a model system, which harbors a simple and well-characterized gut microbiota that is experimentally tractable and has been previously shown to impact host cognition. We established a defined bacterial community-composed of core members of the honey bee gut microbiota. Gnotobiotic bee experiments with the full community, communities missing individual members, or individual members showed that only the full community enhanced honey bees' performances in odor discrimination learning and short-term memory compared to microbiota-deprived bees. Metabolomic analyses identified several metabolites associated with learning success that mapped to pathways modulated by microbial colonization, including tryptophan metabolism, nucleoside metabolism, and lysine degradation. However, many of these metabolites were not altered by removing individual members from the full microbial community. This suggests that microbiota-mediated improvements in cognition are emergent properties of the community as a whole, rather than the result of individual metabolites or specific bacterial taxa acting alone. Our findings support a systems-level view of the microbiome, suggesting that understanding and manipulating host development, particularly in relation to brain function, should prioritize microbial community function (e.g., metabolic pathways) over taxonomic composition alone.},
}

Animals
Bees/microbiology/physiology
*Gastrointestinal Microbiome/physiology
*Cognition/physiology
Memory, Short-Term/physiology
Germ-Free Life
Bacteria/classification

@article {pmid42160397,
year = {2026},
author = {Liu, S and Costa, FS and Valenzano, DR},
title = {Immune surveillance and microbial escape in the aging host: Why does the microbiome lose its balance?.},
journal = {PLoS biology},
volume = {24},
number = {5},
pages = {e3003815},
doi = {10.1371/journal.pbio.3003815},
pmid = {42160397},
issn = {1545-7885},
abstract = {Host-associated microbiomes are compositionally stable across most of the life span, yet undergo consistent and marked deterioration during aging, a phenomenon linked to metabolic dysfunction and disease. What drives this late-life collapse remains poorly understood, in part because the mechanisms by which hosts actively construct and maintain the microbial niche during adulthood remain incompletely characterized. This Unsolved Mystery integrates evidence from immunology and ecosystem ecology to investigate the role of immunosenescence in age-associated dysbiosis, raising the possibility of interventions that restore immune surveillance capacity alongside ecologically informed microbiome management, rather than targeting community composition in isolation.},
}

@article {pmid42160479,
year = {2026},
author = {Catley, CS and Hoedt, EC and Pockney, P and Keely, S and Hedley, KE},
title = {Unravelling Anastomotic Leak: Biological Mechanisms Underlying Intestinal Healing After Resection.},
journal = {American journal of physiology. Gastrointestinal and liver physiology},
volume = {},
number = {},
pages = {},
doi = {10.1152/ajpgi.00071.2026},
pmid = {42160479},
issn = {1522-1547},
support = {//University of Newcastle Australia (UON)/ ; //Australian Government (Federal Government)/ ; G2300020//nswgov | NSW Health (The NSW Health)/ ; },
abstract = {Understanding intestinal healing following resection and anastomosis is a challenging topic due to the complexity of underlying mechanisms. Anastomotic healing follows the fundamental phases of normal wound repair; however, the intestinal anastomosis represents a unique biological environment in which factors such as the structure of the intestines as well as the microbiome, may modify the healing process. Disruptions in any of the healing phases such as the inflammatory, proliferative and remodelling phase may result in severe complications, characterised by the intraluminal contents leaking out into the extraluminal space, termed an anastomotic leak (AL). Despite decades of surgical advancements, we are still no closer in understanding the underlying AL aetiology. It is clear that ALs are multifactorial in nature and contributed to by patient, technical and biological-related factors, however, emerging evidence suggests that biological mechanisms may play a more significant role in AL pathology than originally believed. Evidence points to an interplay between epithelial healing, tissue oxygenation and the resident microbiome in influencing mucosal healing at the anastomotic site. However, the precise contribution of these factors in failed anastomotic healing and AL aetiology remains unclear. In this review, we examine the phases of healing, discuss the existing literature on biological factors affecting anastomotic healing and the advancements made to improve AL rates by targeting the healing response.},
}

@article {pmid42161089,
year = {2026},
author = {Schoenmakers, S and Nieuwenhuijse, DF and Reiss, I and van der Meeren, L and Mulders, CE and Molenkamp, R and Fraaij, PLA and van Boheemen, S},
title = {No detection of relevant virus-specific DNA or RNA sequences in the placenta.},
journal = {Placenta},
volume = {181},
number = {},
pages = {168-174},
doi = {10.1016/j.placenta.2026.05.010},
pmid = {42161089},
issn = {1532-3102},
abstract = {INTRODUCTION: The existence of a placental bacterial microbiome remains a subject of active debate, with recent studies challenging earlier claims of a resident microbial community. While the role of bacterial and viral pathogens in placental infection and adverse pregnancy outcomes is well established, the potential existence of a resident placental (non-pathogenic) virome remains largely unexplored. Given the placenta's vital role in fetal development, our study aimed to investigate whether viral genetic material is present in placental tissue, rather than to identify viral pathogens, in both uncomplicated and complicated pregnancies using viral metagenomic capture sequencing.

METHODS: Placental biopsies were obtained from three pregnancy groups: (1) delivered by elective caesarean section (n = 6), (2) delivered by emergency caesarean section (n = 6), and (3) complicated by preeclampsia (n = 5). Samples were processed using VirCapSeq VERT, a targeted enrichment strategy for vertebrate viruses, followed by Illumina NovaSeq 6000 sequencing.

RESULTS: High quality sequencing yielded an average of 46.6 million reads per sample, with >99.6% of reads aligned to the human genome, and <0.4% of non human sequences. Across all samples, only 12 viral contigs were identified, corresponding to bacteriophages, human endogenous retroviruses, and human gammaherpesvirus 4 (not confirmed by PCR), mostly with low read counts.

CONCLUSIONS: Our study found no evidence supporting the presence of a resident placental virome. Together with existing data on the absence of a bacterial microbiome, these findings support the concept that the placenta does not harbor a detectable microbial or viral community under controlled sampling conditions.},
}

@article {pmid42161263,
year = {2026},
author = {Ni, M and Junker, K and Liu, Y and Fan, Y and Li, Y and Qiao, W and Zhang, XS and Ksiezarek, M and Mead, EA and Tourancheau, A and Jiang, W and Blaser, MJ and Valdivia, RH and Davey, LE and Fang, G},
title = {Epigenetic phase variation in the gut microbiome enhances bacterial adaptation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.019},
pmid = {42161263},
issn = {1934-6069},
abstract = {The human microbiome continuously adapts to variations in diet and host physiology. Epigenetic phase variation (ePV) mediated by bacterial DNA methylation can generate phenotypic heterogeneity within clonal populations. ePVs have been characterized in human pathogens, but their roles in commensals remain unclear. Here, we cataloged ePVs in infant and adult gut microbiomes, revealing genome-wide and site-specific ePV in response to antibiotics and fecal microbiota transplantation. Long-read metagenomics revealed genome-wide ePV mediated by structural variations of DNA methyltransferases. Analysis of public short-read metagenomic datasets further revealed a high prevalence of genome-wide ePVs in the human microbiome. Site-specific ePVs were identified and associated with antibiotics or probiotic engraftment. Focusing on an Akkermansia muciniphila isolate, we find a specific ePV regulating mucC, a gene of unknown function but whose heterologous expression enhances bacterial tolerance to antibiotics via a bet-hedging strategy. Thus, epigenetic modifications are used by gut bacteria to adapt to fluctuating environments.},
}

@article {pmid42161269,
year = {2026},
author = {Hattori-Muroi, K and Maruta, H and Takahashi, D and Kinashi, Y and Hattori, K and Kabumoto, Y and Fujimura, Y and Tsukamoto, S and Suzuki, K and Oguchi, H and Ogihara, Y and Kodaira, Y and Hayashi, E and Takano, K and Komiyama, S and Morita, N and Naganawa-Asaoka, H and Oya, Y and Saito, Y and Ohhashi, W and Kimura, S and Shinkura, R and Matsuda, T and Hase, K},
title = {Dietary soy shapes the microbiome to induce commensal-specific T follicular helper cells and IgA production.},
journal = {Immunity},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.immuni.2026.04.013},
pmid = {42161269},
issn = {1097-4180},
abstract = {The commensal microbiota plays a crucial role in shaping mucosal immunity, particularly in the induction of T follicular helper (Tfh) cells and subsequent B cell IgA production. Here, we demonstrate that dietary soy elicits a robust Tfh cell and IgA response in Peyer's patches of weaning mice. Soy feeding promotes the expansion of two principal commensal bacterial species, Limosilactobacillus reuteri and Muribaculum intestinale. Mechanistically, L. reuteri provides cognate antigens for Tfh cell activation, while M. intestinale functions as an adjuvant by promoting IL-1β production from myeloid cells. The resulting IgA exhibits polyreactivity and enhances protection against Salmonella infection. These findings highlight the specific interplay among dietary components, intestinal microbiota, and mucosal immunity, thereby establishing a diet-microbe-immune axis that shapes host defense in early life. This axis represents a promising therapeutic target for developing future strategies to enhance resistance to enteric pathogens.},
}

@article {pmid42161933,
year = {2026},
author = {Ding, X and Murayama, R and Cai, Y and Yue, Y and Yang, JJ and Hashimoto, K},
title = {Xanomeline-trospium reverses phencyclidine-induced cognitive deficits through modulation of the gut microbiota-brain axis in mice.},
journal = {Translational psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41398-026-04097-0},
pmid = {42161933},
issn = {2158-3188},
support = {U23A20421//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82171189//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Cognitive impairment in schizophrenia remains largely unaddressed by dopamine-based antipsychotics. Xanomeline-trospium (KarXT; Cobenfy[®]), a combination of the muscarinic M1/M4 receptor agonist xanomeline and the peripherally restricted antagonist trospium, effectively reduces psychosis but is associated with gastrointestinal adverse effects. Here, we tested whether KarXT reverses phencyclidine (PCP)-induced cognitive deficits through microbiota-associated mechanisms in adult male mice. Mice received saline or PCP (10 mg/kg/day, s.c.) on days 1-5 and 8-12, followed by vehicle or KarXT [xanomeline 2 mg/kg/day + trospium 1 mg/kg/day, intragastric] on days 15-28. Recognition memory was evaluated using the novel object recognition test (NORT), and lung and intestinal microbiota (small intestine, cecum, and colon) were profiled by 16S rRNA sequencing. KarXT significantly rescued PCP-induced recognition-memory deficits without exacerbating PCP-related reductions in weight gain or fecal output. Microbiome analyses revealed region-specific dysbiosis after PCP exposure, most pronounced in the small intestine and cecum. Several taxa elevated by PCP-including Bacteroides fragilis, Veillonella ratti, Megamonas funiformis, Cupriavidus numazuensis, and Acetanaerobacterium elongatum-were normalized following KarXT treatment. Notably, restoration of multiple pulmonary, cecal, and colonic taxa correlated positively with the NORT recognition index. These findings demonstrate that KarXT reverses PCP-induced cognitive dysfunction while modulating microbial composition in a region-specific manner. Elucidating these relationships may help optimize cognitive efficacy and reduce gastrointestinal adverse effects of muscarinic therapies for schizophrenia.},
}

@article {pmid42162000,
year = {2026},
author = {Zhang, Y and Schuppe-Koistinen, I and Wang, H and Tian, X and Chen, WH and Gao, G and Du, J},
title = {Vaginal microbiome and inflammation cytokines among Chinese women.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00994-w},
pmid = {42162000},
issn = {2055-5008},
support = {82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; 2021-06112//Vetenskapsrådet/ ; 2822//Eurostars/ ; 23 2916 Pj//Cancerfonden/ ; 251172//Radiumhemmets Forskningsfonder/ ; },
abstract = {Human papillomavirus (HPV) infection, cervical intraepithelial neoplasia (CIN), pelvic organ prolapse (POP), cervical polyps, abnormal uterine bleeding, and vaginitis are common gynecological disorders. This study characterized the vaginal microbiome and its cytokine-mediated immune interactions in Chinese women with gynecological disorders. Vaginal swabs from 310 patients diagnosed with gynecological disorders and 112 healthy controls were analyzed via 16S rRNA gene sequencing and cytometric bead array (CBA) to evaluate proinflammatory cytokines. Findings on correlation were validated through in vitro co-culture experiments. HPV infection and CIN were associated with dysbiotic microbial profiles and elevated levels of IL-1α, IL-1β, IL-6, IL-8, MCP-1, and MIG. Stratification by microbial composition demonstrated that HPV/CIN patients with non-Lactobacillus-dominant microbiomes harbored the highest IL-1α and IL-1β concentrations. Validated through computational modeling and in vitro analyses, Lactobacillus crispatus and Lactobacillus iners were identified as being strongly inversely correlated with IL-1α and IL-1β expression. Conversely, non-Lactobacillus taxa, including Bifidobacterium breve, Prevotella bivia, Gardnerella vaginalis, Sneathia amnii, Sneathia sanguinegens, Prevotella amnii, Escherichia coli, and Chlamydia trachomatis, exhibited positive correlations with proinflammatory cytokines. These findings highlight a connection between Lactobacillus species and reduced inflammation, while non-Lactobacillus dominance is linked to increased cytokine-driven responses. This study provides valuable insights into microbiome-immune crosstalk in gynecological diseases.},
}

@article {pmid42162115,
year = {2026},
author = {Ranasinghe, PD and Barazanji, N and Bednarska, O and Bergman Jungeström, M and Lundberg, P and Keita, ÅV and Walter, S and Simon, R},
title = {High-resolution metagenomic characterization of gut microbiota composition and functional pathways in irritable bowel syndrome.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {42162115},
issn = {2045-2322},
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome/genetics ; Female ; *Metagenomics/methods ; Adult ; Middle Aged ; Feces/microbiology ; *Metagenome ; Case-Control Studies ; },
abstract = {Irritable bowel syndrome (IBS) is a common functional gastrointestinal disorder characterized by abdominal pain, altered bowel habits, and frequent comorbidity with anxiety and depression. The gut microbiota has been implicated in gut-brain axis (GBA) dysfunction, but consistent microbial signatures remain unclear. We performed whole metagenome shotgun sequencing of stool samples from 63 female patients with moderate to severe IBS and 34 female healthy controls and assessed microbial composition and functional pathways. Microbial richness and diversity were slightly reduced in IBS, though with high variability and no robust separation from controls. Differential abundance analyses revealed enrichment of Streptococcus sp. and the sulfate-reducing bacterium Desulfovibrio piger in IBS, alongside reductions in Bifidobacterium and Methanobrevibacter. Functional profiling identified 39 differentially abundant pathways: amino acid biosynthesis (e.g., L-isoleucine, L-threonine) was more prominent in IBS, while carbohydrate degradation pathways (e.g., galactose, stachyose) were enriched in healthy controls. These findings indicate modest but significant IBS-associated shifts in gut microbial composition and function that may contribute to IBS symptoms. However, high intra-group variability underscores the complexity of IBS and highlights the need for larger, multi-omics studies to define robust microbial markers. These results contribute to a growing body of evidence emphasizing the complexity of gut microbiota-host interactions and the need for high-resolution, systems-level approaches in microbiome-associated disorders.},
}

Humans
*Irritable Bowel Syndrome/microbiology
*Gastrointestinal Microbiome/genetics
Female
*Metagenomics/methods
Adult
Middle Aged
Feces/microbiology
*Metagenome
Case-Control Studies

@article {pmid42162530,
year = {2026},
author = {Koretz, RL},
title = {JPEN Journal Club 101. Papers from Pharma.},
journal = {JPEN. Journal of parenteral and enteral nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpen.70107},
pmid = {42162530},
issn = {1941-2444},
}

@article {pmid42162563,
year = {2026},
author = {Tang, YY and Zhou, YM and Lin, WK and Zhi, JR and Zou, X},
title = {The role of fungal chitinases in the tripartite interactions among insects, plants and entomopathogenic fungi.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.70955},
pmid = {42162563},
issn = {1526-4998},
support = {//the National Natural Science Foundation of China (Project No.: 32560646),/ ; //the Guizhou Provincial Basic Research Program (Natural Science) (Project number: QianKeHeJiChu-ZK[2024]YiBan002),/ ; //Natural Science Research Project of Colleges and Universities of Guizhou Provincial Department of Education (Youth Science and Technology Talent Development Project) (Project number: QianJiaoJi[2024]34),/ ; //Natural Science Project of Guizhou University (Special Post) (Project number: Gui Da Te Gang He Zi (2022) 51)/ ; //National Science Foundation of China (Project number: 31860507)./ ; },
abstract = {BACKGROUND: Chitinases are ubiquitous hydrolytic enzymes in fungi that specifically degrade chitin, a major structural component of insect exoskeletons and fungal cell walls. Increasing evidence indicates that chitinases play multifaceted roles not only in entomopathogenic fungal infection, but also in plant immune modulation and cross-kingdom interactions. However, their integrative functions within the insect-fungus-plant tripartite system remain insufficiently characterized. This review aims to systematically elucidate the molecular mechanisms and ecological functions of fungal chitinases across multitrophic interactions.

RESULTS: Accumulated studies demonstrate that: Chitinases act as critical virulence factors by facilitating fungal adhesion, cuticle degradation, and host penetration during insect infection; In plant-microbe interactions, chitinases contribute to microbial colonization while simultaneously generating chitin-derived oligomers that function as elicitors to activate plant innate immunity; Within the insect-fungus-plant tripartite system, chitinases mediate resource turnover and signal exchange, thereby shaping complex ecological networks and influencing multilevel biological interactions.

CONCLUSION: Chitinases serve as pivotal molecular hubs linking pathogenicity, symbiosis and ecological regulation across kingdoms. A comprehensive understanding of their multifunctional roles provides critical insights into cross-kingdom interaction mechanisms, and offers promising avenues for advancing biological control strategies, crop resistance improvement and microbial resource exploitation. © 2026 Society of Chemical Industry.},
}

@article {pmid42162574,
year = {2025},
author = {Panneerselvam, R and Karuppannan, M and S C, GP and Durairaj, E},
title = {Impact of Sevoflurane on the Murine Gut Microbiota: Longitudinal Characterization of Diversity Alterations and Dysbiosis Metrics Using Metagenomics.},
journal = {Asian journal of anesthesiology},
volume = {63},
number = {1},
pages = {20-29},
doi = {10.6859/aja.202503_63(1).0003},
pmid = {42162574},
issn = {2468-824X},
mesh = {Animals ; *Sevoflurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; Male ; Mice ; Female ; *Anesthetics, Inhalation/pharmacology ; *Dysbiosis/chemically induced/microbiology ; *Metagenomics/methods ; Feces/microbiology ; Longitudinal Studies ; Sex Factors ; },
abstract = {BACKGROUND: General anesthetics can alter the gut microbiota, but the longitudinal and sex-specific effects of sevoflurane remain unclear. This study examined whether a single exposure to sevoflurane anesthesia induces significant compositional changes in the murine gut microbiome over two weeks, with a secondary focus on sex-specific patterns of alteration.

METHODS: A controlled animal exposure study was conducted at a tertiary-care academic laboratory animal facility in southern India, approved by an institutional animal ethics committee. Twenty albino mice (6-8 weeks old, ~12 g; both females and males) were randomized to sevoflurane or control groups, subdivided by sex. All animals were housed under standard conditions and completed the study protocol. Experimental animals underwent a single 4-hour exposure to sevoflurane in a controlled chamber; controls experienced identical procedures without sevoflurane. Primary endpoints were gut microbiota alpha and beta diversity (Bray-Curtis distance, Shannon, Simpson indices, richness), phylum- and genus-level differential abundance, and derived Firmicutes: Bacteroidetes and Proteobacteria metrics from serial fecal samples across five time points up to Day 14.

RESULTS: Sevoflurane exposure led to significant beta diversity separation between groups at both phylum (P = 0.004) and genus levels (P = 0.034), with additional sex effects (P = 0.035 for genus level); alpha diversity indices were significantly reduced in males (P = 0.0079), but not in females. Phylum-level differential abundance was significant in females but not in males. Group and sex effects were present throughout, and derived dysbiosis metrics varied temporally and by sex Conclusion: A single prolonged exposure to sevoflurane induces significant, durable, and sexually dimorphic shifts in the murine gut microbiome. These findings highlight the importance of considering sex as a biological variable in studies of anesthetic effects on gut health.},
}

Animals
*Sevoflurane/pharmacology
*Gastrointestinal Microbiome/drug effects
Male
Mice
Female
*Anesthetics, Inhalation/pharmacology
*Dysbiosis/chemically induced/microbiology
*Metagenomics/methods
Feces/microbiology
Longitudinal Studies
Sex Factors

@article {pmid42162691,
year = {2026},
author = {Škutová, K and Fišar, Z and Hroudová, J},
title = {Advances in schizophrenia research and treatment: exploring neurotransmitter imbalances, genetics, and innovative therapies.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {},
number = {},
pages = {111749},
doi = {10.1016/j.pnpbp.2026.111749},
pmid = {42162691},
issn = {1878-4216},
abstract = {Schizophrenia is a severe mental disorder arising from genetic vulnerability, impaired neurodevelopment, neurobiological dysregulation, and environmental factors. Its pathophysiology involves disturbances in dopamine, glutamate, and serotonin systems, as well as neuroinflammation, oxidative stress, gut-brain axis dysfunction, and altered energy metabolism. Current dopaminergic pharmacotherapy is often complicated by insufficient efficacy, adverse effects, and patient non-compliance. This review summarizes genetic predispositions, neurotransmitter imbalances, and other contributing factors of schizophrenia, as well as therapeutic advances in novel antipsychotic therapies. Newly developed therapeutic agents preferentially target the serotonergic, muscarinic, glutamatergic, and GABAergic neurotransmitter systems. They include muscarinic agonists, glycine transporter type 1 inhibitors, trace amine-associated receptor 1 agonists, D-amino acid oxidase inhibitors, and agonists or positive allosteric modulators of metabotropic glutamate receptors, and serotonin receptor inverse agonists. Recently, the antipsychotics lumateperone and xanomeline-trospium were approved. Iclepertin, ralmitaront, roluperidone, and brilaroxazine are molecules in Phase 2 or 3 clinical trials. Novel antipsychotic drugs are being developed to effectively treat negative symptoms, cognitive deficits, and total psychopathology in patients with schizophrenia. Adjuvant treatments aimed at mitigating neuroinflammation and oxidative stress; microbiome-targeted interventions, neuroprotective and metabolic agents are being explored. Current research efforts aim to improve treatment outcomes by addressing gaps in antipsychotic therapy and mitigating its adverse effects.},
}

@article {pmid42162728,
year = {2026},
author = {Suresh, G and Nath, M and Tiwari, A and Halder, N and Chawla, R and Velpandian, T},
title = {Gut Microbiome Dysbiosis in Uveitis - Mechanistic Insights and Emerging Therapeutic Strategies.},
journal = {Experimental eye research},
volume = {},
number = {},
pages = {111073},
doi = {10.1016/j.exer.2026.111073},
pmid = {42162728},
issn = {1096-0007},
abstract = {Recent studies have suggested the existence of a gut-eye axis, thus bringing the role of gut microbiota (GM) in the development of ocular inflammation in uveitis into focus. The proposed mechanisms for GM dysbiosis-induced uveitis include molecular mimicry, increased intestinal permeability by disruption of barrier integrity, immunomodulation, and alterations. Data from observational clinical studies indicate distinctive microbial signatures associated with uveal inflammation. Based on these findings, novel therapeutic modalities targeting the GM, such as antibiotics, probiotics, prebiotics, fecal microbiota transplantation, biologics, and dietary interventions have been proposed. While initial studies have shown promising results, there is limited clinical evidence supporting their therapeutic efficiency in the management of uveitis. The complexity and diversity of the GM, along with the lack of controlled clinical trials pose a significant challenge to the development of targeted therapeutics. Additionally, further studies are needed to elucidate the molecular mechanisms linking GM dysbiosis and ocular inflammation for developing specific biomarkers for diagnosis, as well as personalized GM-targeted patient interventions.},
}

@article {pmid42162795,
year = {2026},
author = {Sugimoto, H and Chida, K and Toshimitsu, T and Tokunaga, S and Fujino, K and Kawakami, E},
title = {Associations Between Yogurt Consumption, Gut Microbiota Composition, and Glucose Dynamics: A Single-Arm 84-Day Intervention Study Using Continuous Glucose Monitoring.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101572},
doi = {10.1016/j.tjnut.2026.101572},
pmid = {42162795},
issn = {1541-6100},
abstract = {BACKGROUND: Although yogurt consumption has been associated with favorable metabolic outcomes, its effect on continuous glucose dynamics and gut microbiota composition remains unclear.

OBJECTIVE: To evaluate the effects of daily yogurt intake on glucose dynamics and gut microbiota composition in healthy adults, and to examine baseline host factors associated with inter-individual variability in glycemic response.

METHODS: This single-arm, 84-day intervention study involved 303 Japanese adults without a prior diabetes diagnosis consuming 200 g of plain yogurt daily at breakfast. Continuous glucose monitoring (CGM) was used to assess mean glucose levels, standard deviation (Std), and an autocorrelation-based index (AC_Var). Fecal samples were collected at baseline and post-intervention for 16S rRNA gene sequencing. Associations between baseline clinical, microbial, and genetic characteristics and changes in the CGM-derived measures were evaluated. Differential abundance analysis was used to identify microbial taxa altered by the intervention.

RESULTS: Mean glucose levels decreased progressively, with a reduction of 4.06 mg/dL (95% CI: 2.97 to 5.14) by the final period. Significant decreases were also observed in Std (-0.86 mg/dL; 95% CI: -1.32 to -0.41) and AC_Var (-0.0059; 95% CI: -0.010 to -0.0017). Several baseline gut bacterial genera, including Gemmiger, Veillonella, Alistipes, and Butyricicoccus, were significantly associated with changes in the CGM-derived measures. Following the intervention, increases were observed in the genera Blautia, Faecalibacterium, and Coprococcus, as well as in the phylum Firmicutes, while decreases were noted in Prevotella, Oscillospira, and the phylum Bacteroidetes.

CONCLUSIONS: Daily yogurt consumption was associated with improvements in glucose dynamics and significant remodeling of the gut microbiota. Baseline microbiota profiles were linked to inter-individual differences in glycemic response. These findings suggest the potential role of the gut microbiome in modulating metabolic effects of yogurt and underscore the value of personalized dietary strategies.

UMIN000054094 (https://center6.umin.ac.jp/cgi-open-bin/ctr_e/ctr_view.cgi?recptno=R000061770).},
}

@article {pmid42162796,
year = {2026},
author = {Xie, LX and Xu, QQ and Liu, JY and Zhang, JY and Fu, ZK and Liu, KH and Mao, CR and Deng, FX and Huang, L},
title = {Taurine in Atherosclerosis: A Multi-Target Perspective.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101599},
doi = {10.1016/j.tjnut.2026.101599},
pmid = {42162796},
issn = {1541-6100},
abstract = {Taurine, a conditionally essential amino acid with unique sulfur-containing groups, has many fundamental physiological processes, including osmoregulation and bile acid conjugation. Atherosclerosis (AS) can lead to numerous severe vascular adverse events, such as stroke, coronary artery disease and myocardial infarction, posing a significant threat to human health. Taurine plays a role in multiple targets associated with the development of AS (Figure 1). It regulates lipid metabolism, reduces platelet activation and aggregation, and suppresses uncontrolled proliferation of vascular smooth muscle cells. Additionally, it has antioxidant effects and promotes vascular health through vasodilation and endothelial repair, making it a promising cardiovascular protective agent. Furthermore, its interactions with the gut microbiome offer new insights into its potential for managing pathological conditions that contribute to AS. Current evidence supports that taurine serves as a dietary supplement to enhance both intestinal and cardiovascular health, thereby reducing the risk of AS.},
}

@article {pmid42162932,
year = {2026},
author = {Li, J and Xu, J and Wei, P and Gong, H and Tian, M and Yan, W and Ma, C and Il, D and Yang, Y},
title = {Solid-state fermentation of waste herbal medicine residues by a novel rumen-derived probiotic consortium for valorization and microbial-metabolite shifts.},
journal = {Bioresource technology},
volume = {},
number = {},
pages = {134922},
doi = {10.1016/j.biortech.2026.134922},
pmid = {42162932},
issn = {1873-2976},
abstract = {Compound herbal medicine residues (CHMR) are an underutilized lignocellulosic by-product with potential for conversion into value-added feed. In this study, a rumen-derived probiotic consortium was developed for the solid-state fermentation (SSF) of CHMR, and the associated microbial and metabolic shifts were characterized. A total of 123 bacterial strains were isolated from goat rumen, of which 58 met the criteria for potential feed additives. Bacillus subtilis FB8B and Limosilactobacillus reuteri LA3 were selected as core strains based on cellulolytic activity, acidification capacity, stress tolerance, and growth performance in CHMR. The optimized consortium increased crude protein and flavonoids by 10.87% and 17.99%, respectively, while reducing NDF and ADF by 17.27% and 25.97%, respectively. Integrated 16S rRNA sequencing and untargeted metabolomics showed that inoculated fermentation restructured the bacterial community, enriched beneficial fermentative taxa, and suppressed indigenous competitors. Metabolome reprogramming was characterized by depletion of sugars and amino acids, accumulation of organic acids and phenolic derivatives, and coordinated shifts in pyruvate, amino acid, and secondary metabolite pathways. These findings demonstrate that rumen-derived probiotic fermentation is an effective strategy for CHMR valorization and provide mechanistic insight into microbiome-driven bioconversion of herbal residues into functional feed resources.},
}

@article {pmid42162964,
year = {2026},
author = {Peng, C and Jiang, L and Huang, Z and Wei, X and Zhu, X and Liu, Z and Chen, Q and Shen, X and Gao, P and Jiang, C},
title = {MetaNet: a scalable and integrated tool for reproducible omics network analysis.},
journal = {Bioinformatics (Oxford, England)},
volume = {},
number = {},
pages = {},
doi = {10.1093/bioinformatics/btag321},
pmid = {42162964},
issn = {1367-4811},
abstract = {MOTIVATION: Network analysis has become a central strategy for dissecting complex biological and environmental systems, particularly as modern omics technologies generate increasingly large and heterogeneous datasets. However, current tools often lack the scalability, flexibility, and native multi-omics support required for high-dimensional data analysis. We developed MetaNet, a high-performance R package that unifies network construction, visualization, and analysis across diverse omics layers.

RESULTS: MetaNet enables fast and scalable correlation-based network construction for datasets with more than 10,000 features, providing over 40 layout algorithms, rich annotation utilities, and visualization options compatible with both static and interactive platforms. It further offers comprehensive topological and stability metrics for in-depth network characterization. Benchmarking shows that MetaNet delivers up to a 100-fold improvement in computation time and a 50-fold reduction in memory usage compared to existing R packages. We demonstrate its utility through two representative applications: (1) longitudinal microbial co-occurrence networks revealing airborne microbiome dynamics, and (2) an integrative exposome-transcriptome network of over 40,000 features, uncovering distinct regulatory impacts of biological and chemical exposures. By offering a robust, reproducible, and biologically informed framework, MetaNet advances multi-omics network analysis across biological, ecological, and environmental domains.

AVAILABILITY: MetaNet package is freely available at https://github.com/Asa12138/MetaNet.

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

@article {pmid42163070,
year = {2026},
author = {Mohammed, H and Kohli, I and Lim, HW},
title = {From Ultraviolet to Visible Light: Emerging Concepts in Comprehensive Photoprotection.},
journal = {Photodermatology, photoimmunology & photomedicine},
volume = {42},
number = {3},
pages = {e70098},
doi = {10.1111/phpp.70098},
pmid = {42163070},
issn = {1600-0781},
mesh = {Humans ; *Ultraviolet Rays/adverse effects ; *Sunscreening Agents/therapeutic use ; *Skin/radiation effects/microbiology ; *Light/adverse effects ; *Skin Aging/radiation effects/drug effects ; Erythema/prevention & control/etiology ; *Skin Pigmentation/radiation effects ; },
abstract = {BACKGROUND: Photoprotection has traditionally focused on ultraviolet (UV) radiation, particularly UVB and UVA. Recent evidence highlights the significant role of long-wavelength UVA1 (LW-UVA1, 370-400 nm) and visible light (VL; 400-700 nm) in inducing pigmentation, erythema, and photoaging. This review study summarizes recent advances in LW-UVA1 and VL photoprotection and discusses emerging UV-filter formulations, non-filtering protective ingredients (PINGs), personalized photoprotection, skin microbiome, and environmental considerations.

METHODS: A literature review was conducted using PubMed and Google Scholar online databases to identify recent studies on LW-UVA1 and VL-related photoprotection. Studies were screened for direct relevance to VL and LW-UVA1 and excluded if not available in English, lacked relevance, or had insufficient methodological detail. This review represents a narrative synthesis without formal systematic quality assessment. Results are summarized.

RESULTS: LW-UVA1 and VL exert synergistic effects on the skin, resulting in erythema and sustained pigmentation. Advances include tinted mineral sunscreens with expanding shade ranges, newer UV filters with broader coverage (e.g., Mexoryl 400, TriAsorB), and oral and topical PINGs to be used as potential adjuncts. Environmental concerns for currently used UV filters persist, however. Skin microbiome has also emerged as a target and potential source for novel photoprotective agents. Personalized photoprotection recommendations now provide an individualized approach, taking skin phototype, lifestyle, and risk profile into consideration.

CONCLUSION: Photoprotection is expanding to include a broader-spectrum coverage, including LW-UVA1 and VL with new filters, formulations, and adjuncts. These innovations enhance UV protection, but environmental and long-term safety concerns highlight the need for continued research to ensure safe, effective, and inclusive photoprotection.},
}

Humans
*Ultraviolet Rays/adverse effects
*Sunscreening Agents/therapeutic use
*Skin/radiation effects/microbiology
*Light/adverse effects
*Skin Aging/radiation effects/drug effects
Erythema/prevention & control/etiology
*Skin Pigmentation/radiation effects

@article {pmid42163161,
year = {2026},
author = {Guan, X and Shen, XL and Hao, YN and Dong, ZQ and Chen, JM},
title = {Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.},
journal = {BMC psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12888-026-08132-8},
pmid = {42163161},
issn = {1471-244X},
abstract = {BACKGROUND: Gut microbiota disturbances and impaired mitochondrial function are both linked with the development of major depressive disorder (MDD). However, little is known about how they interact in MDD.

METHODS: We used shotgun metagenomic sequencing to explore fecal microbiome based on 63 MDD patients and 30 healthy controls (HCs). Then we performed GWAS for the discriminative taxonomic features of gut microbiota to identify genetic associations between gut microbiome and mitochondrial DNA (mtDNA) in MDD.

RESULTS: Characteristic gut microbiome-based features, including significant differences in gut microbiota composition and 101 differentially enriched gut microbial species, were found in MDD group vs. HC group. 68 mitochondrial single-nucleotide polymorphisms (mtSNPs) shared between the two groups were identified through GWAS at a Bonferroni-corrected significance level of p < 0.05. The genetic variants and their associated gut microbes were mapped to mitochondrial genome, most of which were located in coding regions, including MT-ND, MT-ND4L, MT-ND5, MT-ND6; MT-CO, MT-CO3; MT-RNR, MT-RNR, and MT-TE. Manhattan plots showed 9 mtSNPs in MDD group and 10 mtSNPs in HC group were associated with 20 gut microbial species at a significance of -log10(p) >20. Furthermore, Sankey diagram was used to visualize the relationships of gut microbiota and mtDNA. 36 mtSNPs (-log10(p) >5) were shown to be associated with 54 gut microbes in crosslinked patterns.

CONCLUSIONS: The current findings provide substantial evidence that complex interactions between gut microbiota and mtDNA contribute to MDD, which enables a better understanding of MDD pathogenesis and suggests new leads for future investigations.

CLINICAL TRIAL NUMBER: ChiCTR2000029703. Registration Date: Feb. 9[th], 2020. Registration Details are available at the website of Chinese Clinical Trial Registry (https://www.chictr.org.cn).},
}

@article {pmid42163413,
year = {2026},
author = {Wang, M and Wang, Y and Bai, M and Peng, Q and Wu, Q and Shang, Z and Chen, G and Zhang, Z and Yang, S and Li, L and Tian, F and Jing, C},
title = {Gut microbiota-derived indole-3-propionic acid promotes lymph node metastasis in gastric cancer via the aryl-hydrocarbon receptor signaling pathway.},
journal = {Cancer & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40170-026-00438-1},
pmid = {42163413},
issn = {2049-3002},
abstract = {BACKGROUND: Gut microbiota (GM) regulates the tumor microenvironment through microbial metabolites. Indole 3-propionic acid (3-IPA) is one such metabolite that regulates gastrointestinal barrier function. In this study, we investigated the effects of 3-IPA on the progression of lymph node metastasis of gastric cancer (GC) and the molecular mechanisms that underlie them.

METHODS: The microbial metabolites were identified using a fecal metabolomic assay in GC patients. Lymphangiogenesis was evaluated using tube formation and wound healing assays in vitro. The expression of aryl hydrocarbon receptor (AHR), CYP1A1, and vascular endothelial growth factor receptor 3 (VEGFR3) were assayed using quantitative real-time PCR (qRT-PCR) and western blot (WB) analyses. Matrigel plug and popliteal lymph node metastasis model were employed to validate the influence on lymphangiogenesis and lymph node metastasis in vivo.

RESULTS: Fecal metabolomic and microbiome profiling was drastically different between GC patients with lymph node metastasis (GC-LM) and those without metastasis. The GC-LM group showed high 3-IPA expression in the feces; 3-IPA had no significant effect on GC cells; Human lymphatic endothelial cells showed greater tube formation and promoted migration after 3-IPA administration. Also, upregulation of AHR, CYP1A1, and VEGFR3 was observed. Moreover, administration of the AHR inhibitor suppressed tube formation and lymph node metastasis both in vitro and in vivo.

CONCLUSIONS: Our findings suggest that gut microbiota-derived 3-IPA functions as a lymph node metastasis promoter through the AHR/CYP1A1-VEGFR3 axis in GC. 3-IPA could serve as a prognostic biomarker and conceivably a therapeutic target for GC lymph node metastasis.},
}

@article {pmid42163541,
year = {2026},
author = {Alhuwaizi, MA and Saloom, HF and Cobourne, M},
title = {Impact of clear aligners and conventional fixed orthodontic appliances on oral hygiene and periodontal health: A systematic review with GRADE assessment of the certainty of evidence.},
journal = {European journal of orthodontics},
volume = {48},
number = {3},
pages = {},
doi = {10.1093/ejo/cjaf100},
pmid = {42163541},
issn = {1460-2210},
mesh = {Humans ; *Oral Hygiene ; *Orthodontic Appliances, Fixed/adverse effects ; *Oral Health ; Randomized Controlled Trials as Topic ; Periodontal Diseases/etiology ; *Orthodontic Appliances, Removable/adverse effects ; Periodontal Index ; },
abstract = {BACKGROUND: The use of clear aligners (CA) has exponentially increased in the last decades due to their superior esthetic, ease of use and cleaning, and comfort in comparison to conventional fixed appliance (FA). However, prolonged wearing of CA could also alter oral microbiome and adversely affect oral hygiene and periodontal health.

OBJECTIVE: To assess oral hygiene level and periodontal health status in patients treated with CA versus those treated with FA using a combination of risk of bias (RoB) and Grading of Recommendations Assessment, Development and Evaluation (GRADE) tools.

SEARCH METHODS: A comprehensive electronic search was conducted in four databases, including Scopus, PubMed, Web of Science, and Google Scholar, to retrieve relevant randomized controlled trials (RCTs) in the last 10 years from 2015 to April 2025.

SELECTION CRITERIA: The study aimed to include RCTs that focused on the impact of CA and FA orthodontic treatments on oral hygiene and periodontal health.

DATA COLLECTION AND ANALYSIS: Independent eligibility assessment, data extraction, and filtering process were performed. The RoB 2 tool was used to assess the quality of the included RCTs. Data relating to oral hygiene/periodontal health assessed by different clinical periodontal indices (primary outcome) and other findings (secondary outcomes) were extracted. Certainty of evidence was determined using GRADE system.

RESULTS: Initial search process yielded 1098 records which were assessed for eligibility, screened according to titles, abstracts, and full-text reading. Six RCTs were found eligible for analysis and included for synthesis of evidence. Qualitative analyses of the included RCTs showed that periodontal parameters were significantly better in patients treated with CA than with FA. Five RCTs exhibited high RoB together with overall inconsistencies in the given oral hygiene instructions, age, follow-up, diagnosis, and measurements. Certainty of evidence ranged from very low for oral hygiene level and low for periodontal health.

CONCLUSIONS: Dual quality assessment indicated that the advantages of CA over FA in terms of oral hygiene and periodontal health are highly compliance dependent. However, due to heterogeneities, high RoB, and low to very low certainty of evidence in current RCTs, outlining a firm conclusion was impeded.

REGISTRATION: PROSPERO (CRD420251120933).},
}

Humans
*Oral Hygiene
*Orthodontic Appliances, Fixed/adverse effects
*Oral Health
Randomized Controlled Trials as Topic
Periodontal Diseases/etiology
*Orthodontic Appliances, Removable/adverse effects
Periodontal Index

@article {pmid42163554,
year = {2026},
author = {Hamid, NH and Karim, MMA and Daud, HM and Hamdan, RH and Yusoff, SFM},
title = {A Stage-Aligned Disease Management Framework for Aeromonas hydrophila in Aquaculture: Implications for Antimicrobial Stewardship.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70211},
doi = {10.1111/jfd.70211},
pmid = {42163554},
issn = {1365-2761},
abstract = {Aeromonas hydrophila remains a persistent challenge in freshwater aquaculture despite extensive research and the availability of multiple disease-control strategies. Although antibiotics are widely used, alternative approaches including probiotics, immunostimulants, vaccines and bacteriophages are often evaluated in isolation. Increasing evidence indicates that disease outbreaks are not driven by pathogen presence alone, but by dynamic interactions among host condition, environmental stability and pathogen virulence. This review synthesises evidence from 45 controlled intervention studies to propose a stage-aligned framework for managing A. hydrophila, in which disease progression reflects increasing system instability. Stage I (Baseline Prevention) focuses on biosecurity, water quality management and microbiome stability. Stage II (Immune Priming) addresses early risk conditions characterised by elevated stress and immune responses alongside increasing pathogen load, where immune modulation, functional feeds and prophylactic vaccination enhance host resilience. Stage III (Containment) involves targeted interventions, including bacteriophage application, environmental correction and strengthened biosecurity to limit pathogen amplification and transmission. Stage IV (Emergency Control) represents acute outbreak conditions requiring integrated responses, including disinfectant application, emergency biosecurity measures and diagnosis-guided antibiotic use where legally permitted. Reported relative percent survival (RPS) varies substantially between laboratory and field conditions, highlighting the context-dependent performance of interventions. By prioritising intervention timing and system condition over intrinsic tool efficacy, this framework supports reduced antimicrobial reliance while maintaining production stability in intensive aquaculture systems.},
}

@article {pmid41965837,
year = {2026},
author = {Munoz Briones, J and Ball, BK and Jena, S and Lescun, TB and Chan, DD and Brubaker, DK},
title = {Rumenomics: evaluation of rumen metabolites from healthy sheep identifies differentially produced metabolites across sex, age, and weight.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {41965837},
issn = {2524-4671},
support = {DGE-1842166//National Science Foundation/ ; W911NF2110372//Defense Sciences Office, DARPA/ ; },
abstract = {BACKGROUND: The rumen harbors a diverse and dynamic microbiome vital in digesting vegetation into metabolic byproducts for energy and general biological function. Although previous studies have reported connections between the rumen and the overall health of the sheep, the exact biological process by which this occurs is not well understood. Therefore, our study aimed to quantify sheep rumen metabolites to determine if enriched biological pathways are differentiable across phenotypic features of sex, age, and weight.

RESULTS: We collected and quantified metabolites of rumen samples from sixteen sheep using liquid chromatography-tandem mass spectrometry. We performed a series of univariate and multivariate statistical analyses to interpret the rumen metabolomics data. To identify metabolic pathways associated with the phenotypic features of sex, weight, and age, we used MetaboAnalyst, which identified amino acid metabolism as a distinguishing factor. Among the pathways, phenylalanine metabolism emerged as a key pathway differentiating sheep based on sex and age. Additionally, phenylalanine, tyrosine, and tryptophan biosynthesis were exclusively associated with age. In univariate linear models, we also discovered that these amino acid and protein pathways were associated with weight by age-corrected effect. Finally, we identified arginine and proline biosynthesis as a pathway linked to metabolites with weight.

CONCLUSION: Our study identified differential pathways based on the sex, age, and weight features of sheep. Metabolites produced by the rumen may act as an indicator for sheep health and other ruminants. These findings encourage further investigation of the differentially produced metabolites to assess overall sheep health.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s42523-026-00558-5.},
}

@article {pmid41968333,
year = {2026},
author = {Chen, C and He, J and Ma, Z and Na, W and Cao, Y and Li, B and He, Z and Yuan, H and Xiao, H and Wang, S and Liu, R and Yu, S and Kang, L},
title = {Sex differences in behaviors, neuronal activation, and gut-microbiota-metabolic axis in a repeated nitroglycerin-induced chronic migraine model.},
journal = {The journal of headache and pain},
volume = {27},
number = {1},
pages = {},
pmid = {41968333},
issn = {1129-2377},
support = {82201365//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Migraine is a debilitating primary headache disorder characterized by significant sex differences in epidemiology, clinical features, comorbidities, and treatment response, yet the underlying mechanisms remain obscure. This study aims to dissect the sex difference map in chronic migraine models and explore the underlying mechanisms driving these specific phenotypes.

METHODS: A mouse model of chronic migraine was established by intraperitoneal injection of nitroglycerin (NTG, 10 mg/kg, 5 times in 9 days). Both male and female mice were included. Mechanical withdrawal thresholds (MWTs) were measured to assess migraine-related hyperalgesia. Anxiety-like behaviors and acute malaise were evaluated using the Open Field Test (OFT), Elevated Plus Maze (EPM), and Light-Dark Box (LDB). Neuronal activation was mapped via c-Fos immunofluorescence. Medullary TNF-α levels were quantified by ELISA. 16S rRNA sequencing and targeted metabolomics characterized the gut microbiota composition and fecal metabolites, respectively.

RESULTS: Although male and female mice showed comparable responses in acute and chronic mechanical pain hyperalgesia, significant sex differences were observed in other migraine-like behaviors: only male mice exhibited significant acute-phase motor inhibition and anxiety-like behavior in the chronic phase. These phenotypic differences coincided with a male-restricted elevation of medullary TNF-α following NTG administration. In terms of regional brain activation, the AP stood out in males for its markedly elevated c-Fos cell. This sexual dimorphism extended to the gut-brain axis: while the female NTG group microbiome was enriched with g-Akkermansia, the male profile was dominated by g-Parabacteroides. Metabolomic profiling identified 29 differential metabolites (NTG vs. VEH) in males but only 3 in females. In males, these alterations were primarily enriched in the pentose and glucuronate interconversions and biosynthesis of unsaturated fatty acids pathways that are involved in neuropsychiatric disorders.

CONCLUSION: The NTG-induced chronic migraine model exhibits significant sexual dimorphism, with male mice showing greater sensitivity to acute discomfort and chronic emotional comorbidities. This exploratory study identifies the specific activation of the AP brain region, medullary neuroinflammation, and more severe disturbances in the gut microbiota-metabolic axis as potential contributors to this sex-dependent phenotype.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s10194-026-02360-9.},
}

@article {pmid42148582,
year = {2026},
author = {Yu, L and Li, H and Yu, H and Zhou, Y and Wang, X and Luo, L},
title = {Inoculation of Bacillus velezensis SD24 enhancing the accumulation of tea catechin secondary metabolites.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0346925},
doi = {10.1128/spectrum.03469-25},
pmid = {42148582},
issn = {2165-0497},
abstract = {Tea (Camellia sinensis) is a globally significant economic crop, and its desirable quality and health benefits are largely credited to catechin derivatives. Plant growth-promoting rhizobacteria (PGPR), such as Bacillus velezensis, are well-known for enhancing the environmental fitness and disease resistance of plants. However, the regulation of their impact on tea catechin biosynthesis remains unclear. While previous studies have focused on PGPR-facilitated growth promotion in crops like tomatoes and rice, the physiological mechanisms by which microbes regulate secondary metabolism in tea-especially under co-inoculation conditions-remain largely underexplored. This study examined the effects of B. velezensis SD24, isolated from tea rhizosphere soil, on catechin derivative accumulation of tea leaves by altering gene expression and the rhizosphere microbiome. Strain SD24 exhibited broad-spectrum antimicrobial activity against various pathogens due to behaving antimicrobial gene clusters. Tea plants inoculated with SD24 showed significantly increased levels of catechin derivatives in their leaves. This was likely achieved by upregulation of leucoanthocyanidin reductase and anthocyanidin reductase within the phenylpropanoid pathway. Additionally, chlorophyll content was increased. Transcriptomic analysis revealed a notable enrichment in biosynthesis of secondary natural products among the tea genes activated by SD24 inoculation. Metagenomic analysis further demonstrated that SD24 inoculation led to a restructuring of the tea rhizosphere microbiome. Notably, co-inoculation with Piriformospora indica, a beneficial endophytic fungus, suppressed SD24-induced gene expression and catechin accumulation, underscoring its antagonism toward SD24. These findings suggest that B. velezensis SD24 enhances tea quality, probably by transcriptionally activating the synthesis of catechin derivatives, a process associated with the restructuring of the rhizosphere microbiome.IMPORTANCEThe mechanisms through which plant growth-promoting rhizobacteria (PGPR) influence secondary metabolism in perennial crops remain poorly understood. This study demonstrates that Bacillus velezensis SD24, a tea rhizosphere isolate, significantly enhances the accumulation of health-beneficial catechin derivatives in tea leaves. This quality improvement is associated with transcriptionally upregulating key biosynthetic genes (LAR and ANR) and concurrently restructuring the rhizosphere microbiome. Furthermore, we reveal a critical antagonistic interaction, where the beneficial fungus Piriformospora indica suppresses these SD24-induced effects. Our findings provide crucial insights into how specific PGPR strains may directly enhance tea quality by affecting host plant metabolism and the root microbiome, highlighting the complex and tailored microbial interactions that could be harnessed for sustainable agriculture.},
}