@article {pmid42998020,
year = {2026},
author = {Saedi, N and Zhang, S and Lund, MS and Cai, Z and Karaman, E},
title = {Microbiome-Informed Genomic Prediction of CH4:CO2 Ratio in Holstein Dairy Cattle Using 16S rRNA Profiles and SNP Markers.},
journal = {Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie},
volume = {},
number = {},
pages = {},
doi = {10.1111/jbg.70086},
pmid = {42998020},
issn = {1439-0388},
support = {1115-00023B//Innovationsfonden/ ; },
abstract = {Ruminant animals produce methane as a by-product of microbial fermentation in the rumen, with cattle being the largest contributors among ruminants. Methane emissions may be influenced directly by the host's genetics and indirectly through host-mediated effects on rumen microbiome composition. In this study, we investigated whether modelling both direct and indirect genetic effects could improve the genomic prediction of breeding values for methane emissions. We used genotype, methane CH4:CO2 ratio and 16S rRNA gene amplicon sequencing data (16S), including 16S genus (16S-G), 16S species (16S-S) from Danish Holstein cows. A conventional genomic best linear unbiased prediction (GBLUP) model was used as a benchmark and compared with a microbiome-informed GBLUP approach based on three linked linear mixed models for the prediction of breeding values. In GMBLUP, the first model regresses methane emissions on three random animal effects (archaeal 16S, bacterial 16S and polygenic effects) using corresponding microbiome and genomic relationship matrices. The second and third models separately regress archaeal and bacterial 16S on random animal effects defined by the genomic relationship matrix. We evaluated prediction accuracy using five-fold cross-validation. The GBLUP model, which used only genomic marker information, achieved a mean accuracy of 0.20 across the five folds when evaluated in the animal subsets corresponding to the 16S-G and 16S-S datasets, while GMBLUP showed higher accuracy, particularly for the 16S-G dataset, with a mean accuracy of 0.48. These results highlight that incorporating microbiome information into genomic prediction models may improve predictive performance for the CH4:CO2 ratio, although further validation in larger and independent populations is required before practical implementation in breeding programmes.},
}

@article {pmid42998127,
year = {2026},
author = {Psyllia, D and Stylianakis, D and Denaro, N and Pistis, M and Lambertini, M and Lai, E and Molozzu, D and Psyllia, MM and Stylianakis, I and Stochino, ME and Chillotti, C and Scartozzi, M and Petrelli, F and Solinas, C},
title = {Antibiotic Exposure and Treatment Outcomes in Head and Neck Squamous Cell Carcinoma and Nasopharyngeal Carcinoma: A Systematic Review and Meta-Analysis.},
journal = {Current oncology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42998127},
issn = {1534-6269},
mesh = {Humans ; *Anti-Bacterial Agents/therapeutic use/adverse effects ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/therapy/mortality ; *Nasopharyngeal Carcinoma/drug therapy/mortality/therapy ; Treatment Outcome ; *Nasopharyngeal Neoplasms/drug therapy ; Immune Checkpoint Inhibitors/therapeutic use ; Chemoradiotherapy ; },
abstract = {PURPOSE OF REVIEW: Systemic antibiotics may disrupt the gut and oral microbiome, potentially affecting anticancer treatment efficacy. Their prognostic relevance in head and neck squamous cell carcinoma (HNSCC) and nasopharyngeal carcinoma (NPC), particularly during immune checkpoint inhibitor (ICI)-based therapy or definitive chemoradiotherapy (CRT), remains uncertain. This systematic review and meta-analysis evaluated associations between systemic antibiotic exposure around treatment initiation and oncologic outcomes.

METHODS: PubMed/MEDLINE, Embase, and Scopus were searched from January 2015 to March 28, 2026. Eligible studies included patients with HNSCC or NPC receiving ICI, definitive CRT, or chemo-immunotherapy and reporting overall survival (OS), progression-free survival (PFS), or objective response rate (ORR). Random-effects models pooled hazard ratios (HRs) and 95% confidence intervals (CIs) for OS and PFS; ORR was synthesized descriptively. Risk of bias was assessed, as appropriate, using ROBINS-I, ROBINS-E, RoB 2, or the Newcastle-Ottawa Scale.

RESULTS: Eleven studies involving 6,293 patients were included; nine studies (4,507 patients) contributed to survival meta-analyses. Antibiotic exposure was associated with worse OS (HR 1.78, 95% CI 1.52-2.08) and PFS (HR 1.58, 95% CI 1.28-1.96). Associations were consistent in ICI-treated cohorts (OS HR 1.80, 95% CI 1.53-2.13; PFS HR 1.67, 95% CI 1.24-2.25) and CRT cohorts (OS HR 1.73, 95% CI 1.29-2.32; PFS HR 1.53, 95% CI 1.11-2.11). Heterogeneity was low-to-moderate for OS (I2=28.6%) and negligible for PFS (I2=0%). Leave-one-out analyses showed stable OS (HR range 1.76-1.86) and PFS estimates (1.58-1.63). Worse OS was observed for both 30-60-day pre-ICI exposure (HR 2.04, 95% CI 1.43-2.90) and concurrent/peri-treatment exposure (HR 1.74, 95% CI 1.49-2.04). ORR was descriptively lower in antibiotic-exposed patients. Most studies had serious/high risk of bias, primarily due to confounding by indication.

CONCLUSIONS: Systemic antibiotic exposure around treatment initiation is associated with inferior survival and response in HNSCC and NPC. However, predominantly observational evidence and substantial confounding preclude causal inference. Prospective microbiome-informed studies are needed.},
}

Humans
*Anti-Bacterial Agents/therapeutic use/adverse effects
*Squamous Cell Carcinoma of Head and Neck/drug therapy/therapy/mortality
*Nasopharyngeal Carcinoma/drug therapy/mortality/therapy
Treatment Outcome
*Nasopharyngeal Neoplasms/drug therapy
Immune Checkpoint Inhibitors/therapeutic use
Chemoradiotherapy

@article {pmid42998368,
year = {2026},
author = {Dall, SM and Møllekær, AH and Kousgaard, SJ and Jakobsen, SS and Larsen, L and Sørensen, B and Thorlacius-Ussing, O and Albertsen, M},
title = {Microbial and antimicrobial resistance signatures differentiate healthy and inflamed ileal pouches in patients with ulcerative colitis.},
journal = {Journal of Crohn's & colitis},
volume = {20},
number = {11},
pages = {},
pmid = {42998368},
issn = {1876-4479},
support = {81-A.21//Svend Andersen Fonden/ ; 10.46540/4308-00176B//Independent Research Fund Denmark/ ; 101078234//European Union/ ; },
mesh = {Humans ; *Colitis, Ulcerative/microbiology/surgery ; *Pouchitis/microbiology ; Female ; *Colonic Pouches/microbiology ; Male ; Feces/microbiology ; Adult ; Middle Aged ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUND AND AIMS: Fecal microbiota transplantation (FMT) from healthy donors with a normally functioning colon has limited clinical effect in the treatment of chronic pouchitis. However, a normally functioning ileal pouch-anal anastomosis (IPAA) physiology differs from individuals with a healthy intact colon. We aimed to investigate the microbial characteristics of patients with a normally functioning IPAA (HealthyPouch) compared with chronic pouchitis (SickPouch), ulcerative colitis (UC), and a healthy intact colon microbiome (NormalGut). Furthermore, we investigated how repeated antibiotic use influences antimicrobial resistance on a bacterial genome level.

METHODS: Fecal samples from 190 participants were collected; HealthyPouch (n = 38), SickPouch (n = 37), UC (n = 23), and NormalGut (n = 92) and sequenced with Illumina and taxonomically profiled. Samples from HealthyPouch, SickPouch, and NormalGut were also long-read sequenced using Oxford Nanopore Technologies for reconstruction of 12 282 metagenome-assembled genomes (MAGs). DNA methylation motifs were used for plasmid-host association.

RESULTS: The HealthyPouch microbiome is distinct from both the UC, NormalGut, and SickPouch microbiome. Escherichia coli MAGs in the SickPouch (n = 21) microbiome had significantly higher co-occurring ciprofloxacin resistance mutations in the gyrA and parC genes, compared to both HealthyPouch (n = 26; BH adjusted P < .05) and NormalGut (n = 40; BH adjusted P < .05). Based on DNA methylation pattern, three plasmids were associated with E. coli carrying extended-spectrum beta lactamase genes.

CONCLUSIONS: HealthyPouch microbiota differs from NormalGut microbiota, and could therefore be more appropriate for FMT treatment of chronic pouchitis. The association between E. coli and resistance gene-carrying plasmids underscores the importance of integrating plasmid analysis into metagenome-based approaches for personalized antibiotic treatment and resistance monitoring.},
}

Humans
*Colitis, Ulcerative/microbiology/surgery
*Pouchitis/microbiology
Female
*Colonic Pouches/microbiology
Male
Feces/microbiology
Adult
Middle Aged
Anti-Bacterial Agents/therapeutic use
*Gastrointestinal Microbiome/genetics
*Drug Resistance, Bacterial/genetics
Escherichia coli/genetics
Fecal Microbiota Transplantation

@article {pmid42998537,
year = {2026},
author = {Chu, Y and Qian, Y and Shi, J and Hu, M and Ling, R and Wu, Y and Dai, H and Yan, Z and Xian, Q and Chen, H and Jiang, H and Zhu, W},
title = {Fecal microbiota capsule transplantation plus immunotherapy as first-line maintenance therapy for patients with malignant solid tumors: A single-arm, dose-escalation, exploratory phase I study.},
journal = {Translational oncology},
volume = {75},
number = {},
pages = {103106},
doi = {10.1016/j.tranon.2026.103106},
pmid = {42998537},
issn = {1936-5233},
abstract = {BACKGROUND: Chemotherapy combined with programmed cell death protein-1 (PD-1) antibody immunotherapy has become the standard first-line treatment for most patients with malignant solid tumors. However, data from multiple phase III trials indicate that even with first-line induction followed by immunotherapy maintenance, median progression-free survival (PFS) remains less than one year.

METHODS: In this phase I dose-escalation trial (3 + 3 design), 12 patients who completed six cycles of first-line chemoimmunotherapy received oral fecal microbiota transplantation (FMT) capsules plus anti-PD-1 maintenance immunotherapy at escalating dose levels (i to i + 3). The primary endpoint was safety; secondary endpoints included the recommended phase II dose (RP2D), PFS, and disease control rate (DCR). Fecal and blood samples were collected for exploratory microbiome and metabolomic analyses.

RESULTS: No grade ≥3 FMT-related toxicities occurred. With a median follow-up of 36.9 months, median PFS was 19.8 months (95% CI 11.2-28.4); maintenance-phase PFS was 11.7 months (95% CI 4.1-19.3). 4 patients remained progression-free on continued immunotherapy. Four patients (33.3%) experienced grade 1-2 gastrointestinal events. Microbiomic analyses showed post-FMT expansion of Blautia and Faecalibacterium, with dose level i + 1 demonstrating the greatest α-diversity shift and engraftment rate. Metabolomic analysis showed that serum arachidonic acid levels increased after FMT.

CONCLUSION: Oral FMT combined with immunotherapy as first-line maintenance therapy for solid tumors was safe and well tolerated, showed promising preliminary efficacy, and induced favorable compositional changes in the gut microbiota. This study was registered with the Chinese Clinical Trial Registry (Registration No.: ChiCTR2100054928).},
}

@article {pmid42998587,
year = {2026},
author = {Leone, L and Papale, M and Appolloni, L and Cattaneo, A and Abbamondi, GR and Tommonaro, G and Lo Giudice, A and Chianese, E and Poli, A and Finore, I and Di Donato, P},
title = {From community profiling to functional insights: bacterial populations in marine sediments from an Antarctic Specially Protected Area (Terra Nova Bay, Ross Sea, Antarctica).},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128811},
doi = {10.1016/j.micres.2026.128811},
pmid = {42998587},
issn = {1618-0623},
abstract = {Marine sediments remain among the least characterised components of the Antarctic microbial landscape. Here, bacterial communities were investigated in sediments from three sites within the Antarctic Specially Protected Area No. 161, in Terra Nova Bay (Ross Sea, Antarctica). Samples were collected during the XXXIII Italian Antarctic Expedition. The sites differed in their local environmental context, including proximity to the Adélie penguin colony and Mario Zucchelli Station. Bacterial communities were characterised by 16S rRNA gene sequencing (V3-V4 region), with amplicon sequence variants resolved using DADA2, and complemented by PICRUSt2 predicted functional potential, bacterial isolation, and quorum-sensing bioassays. Bacteroidota and Proteobacteria dominated all sites, but community composition and diversity differed significantly among sampling sites. AC showed the highest alpha diversity, while ASPA2 showed the lowest. Of the 5423 amplicon sequence variants detected across the nine samples (three per site), 680 were shared across all samples and defined a core microbiome dominated by Bacteroidota and Proteobacteria. Despite marked differences in community composition, broad predicted functional profiles were relatively conserved, whereas finer-scale KEGG Orthology profiles showed site-associated variation. Seventeen psychrophilic strains were isolated, predominantly Psychrobacter, and most displayed hydrolytic activity towards olive oil, tributyrin, or both substrates. Biosensor-responsive activity was detected exclusively in enrichment cultures and not in extracts from individual isolates, providing preliminary evidence of putative quorum-sensing-related activity associated with mixed microbial consortia. These findings provide a baseline for investigating environmental drivers of Antarctic sediment microbiomes and microbial interactions in future studies.},
}

@article {pmid42998756,
year = {2026},
author = {Farhadi, L and Khalil, N and Kowalczyk, W and Lio, P and Yosipovitch, G},
title = {Bacteriophage-Derived Endolysins in Atopic Dermatitis and Other Pruritic Dermatoses: Mechanistic Rationale, Clinical Evidence, and Limitations.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.10.037},
pmid = {42998756},
issn = {1523-1747},
abstract = {Chronic pruritus in atopic dermatitis (AD) is associated with cutaneous dysbiosis, including loss of protective commensals and expansion of Staphylococcus aureus. S. aureus can promote itch through secreted proteases and toxins that activate sensory neurons and amplify type 2 inflammation. Because broad-spectrum antimicrobials may disrupt commensal communities, bacteriophage-derived endolysins have been proposed as a more targeted approach. These enzymes cleave bacterial peptidoglycan and can rapidly lyse susceptible bacteria without requiring active growth, although their antimicrobial spectrum varies by enzyme. Preclinical studies support selective antistaphylococcal activity, but early clinical findings in AD are mixed. Therefore, endolysins should be considered alongside other microbiome-directed approaches, including topical bacteriotherapy with protective commensals. This review evaluates how endolysins work, the available clinical evidence, and the remaining questions about formulation, patient selection, inflammation caused by rapid bacterial breakdown, and toxins that may remain active after the bacteria are killed.},
}

@article {pmid42998821,
year = {2026},
author = {Bai, Y and Li, ZB and Dong, PY and Feng, YN and Zhang, XF and Zhang, BQ and You, W},
title = {Multi-omics studies show that naringin improves cyclophosphamide-induced testicular and intestinal damage by enhancing energy metabolism.},
journal = {The Journal of steroid biochemistry and molecular biology},
volume = {},
number = {},
pages = {107142},
doi = {10.1016/j.jsbmb.2026.107142},
pmid = {42998821},
issn = {1879-1220},
abstract = {Cyclophosphamide (CTX) is an anticancer agent that severely impairs male reproductive health. Naringin (NAR), a flavonoid compound, has the potential to ameliorate CTX-induced damage; however, the underlying mechanisms remain unclear. In this study, an integrative approach combining transcriptomics, microbiome analysis, and serum metabolomics was employed to comprehensively evaluate the protective effects of NAR on reproductive function in CTX-treated mice. Microbiome analysis revealed that NAR restored CTX-induced alterations in gut microbial composition. Metabolomic profiling demonstrated that NAR stabilised cholesterol metabolism and primary bile acid biosynthesis, increased serum choline levels, and alleviated reproductive dysfunction in CTX-exposed mice. Transcriptomic analyses of the testes and intestine indicated that NAR modulated glycolysis and the MAPK signalling pathway in CTX-treated mice. Validation of serum metabolites further supported their role in promoting intestinal and testicular development. Research indicates that naringin ameliorates cyclophosphamide-induced reproductive risks in males, partly due to its enhancement of energy metabolism.},
}

@article {pmid42998838,
year = {2026},
author = {Bongers, KS},
title = {The impact of the gut microbiome on skeletal muscle in health and disease.},
journal = {The American journal of the medical sciences},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.amjms.2026.11.009},
pmid = {42998838},
issn = {1538-2990},
abstract = {The gut microbiome, the community of bacteria residing the lower gastrointestinal tract, is increasingly recognized as an important influence on skeletal muscle physiology, with critical implications for muscle disorders such as sarcopenia and muscular dystrophy. Researchers have uncovered multiple microbiome-derived metabolites that alter skeletal muscle protein synthesis, mitochondrial biogenesis, protein degradation, and glucose transport. Moreover, the microbiome mediates systemic cytokine release of interleukin-6 and tumor necrosis factor alpha, which can drive muscle loss. These studies have led to the identification of gut bacterial species (such as Veillonella atypica and Roseburia inulinivorans) that improve muscle endurance and strength when administered as probiotics in animal models. Several clinical trials of microbiome-focused therapies have also been conducted, with suggestion of benefits as well as potential harms. Taken together, the gut microbiome plays a key role in modulating skeletal muscle physiology, and may serve as the basis for novel therapeutics targeting muscle disease.},
}

@article {pmid42999037,
year = {2026},
author = {Madamanchi, K and Gurrala, S and Watson, J and Melkani, G},
title = {Gut microbiome depletion aggravates glial-mediated Alzheimer's disease pathology through inflammatory, metabolic, and proteostatic dysregulation.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2753247},
doi = {10.1080/19490976.2026.2753247},
pmid = {42999037},
issn = {1949-0984},
mesh = {Animals ; *Alzheimer Disease/microbiology/metabolism/pathology/physiopathology ; *Neuroglia/metabolism/pathology ; Humans ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; Amyloid beta-Peptides/metabolism ; Proteostasis ; Brain/metabolism/pathology ; Drosophila ; Drosophila melanogaster ; Bacteria/classification/isolation & purification/genetics ; Inflammation ; },
abstract = {Alzheimer's disease (AD) is a progressive neurodegenerative disorder characterized by chronic neuroinflammation, metabolic dysfunction, and impaired proteostasis. Emerging evidence suggests that the gut microbiome influences brain function through the gut-brain axis; however, the mechanisms by which this communication affects AD pathology remain poorly understood. In this study, we used humanized Drosophila AD models expressing human AD-related transgenes in glial cells to investigate how glial AD pathology influences the gut microbiome and how microbiome depletion affects behavior and disease progression. Our findings revealed significant alterations in the abundance of several gut microbial taxa, including Lactobacillus, Acetobacter, Enterococcus, Enterobacter, Pseudomonas, Leuconostoc, Providencia, and Gluconobacter, suggesting a potential interaction between the gut microbiome and AD progression. To further define the role of the gut microbiome in AD progression, we treated Drosophila with antibiotics to achieve substantial microbiome depletion (SMD) and evaluated the resulting behavioral, physiological, and molecular changes. Compared with conventional controls, flies with SMD exhibited enhanced inflammatory signaling and cell death, impaired autophagy, lipid dysregulation, and increased accumulation of amyloid β-42 (aβ42) and phospho-tau (pTau), with the extent of these changes varying among the different humanized AD models. These molecular alterations further exacerbated sleepcircadian disruption, altered locomotor performance, and worsened learning and memory deficits. Furthermore, we demonstrated a link between enhanced neuroinflammation and the accumulation of aβ42, pTau, and amyloid precursor protein (APP) proteins. Collectively, our findings demonstrate that gut microbiome depletion aggravates glial-mediated AD pathology through the coordinated disruption of inflammatory, metabolic, and proteostatic pathways, ultimately leading to behavioral dysfunction. These results identify the gut microbiome as a critical regulator of glial homeostasis and provide new insights into its contribution to the progression of neurodegenerative disorders.},
}

Animals
*Alzheimer Disease/microbiology/metabolism/pathology/physiopathology
*Neuroglia/metabolism/pathology
Humans
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
Amyloid beta-Peptides/metabolism
Proteostasis
Brain/metabolism/pathology
Drosophila
Drosophila melanogaster
Bacteria/classification/isolation & purification/genetics
Inflammation

@article {pmid42999040,
year = {2026},
author = {Sadegi, M and Johnson, BB and Sanches, TM and Ang, G and Cao, J and Ambre, M and Brennan, M and George, O and Knight, R and Baud, A and Palmer, AA and Polesskaya, O},
title = {Replication of Host St6galnac1 -Microbiome Association Across Distinct Experimental Conditions in Heterogeneous Stock Rats.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.09.758003},
pmid = {42999040},
issn = {2692-8205},
abstract = {The gut microbiome is shaped by both environmental and host genetic factors. Identifying specific host loci is essential for understanding the heritability of microbiome-associated traits. The gene St6galnac1 encodes a sialyltransferase involved in mucin O-glycosylation. Tonnelé et al. (2025) identified significant associations between a locus containing St6galnac1 gene, and the abundance of genus Paraprevotella using cecal samples collected from fasted animals. This association was replicated across three cohorts, and paralleled with association found in humans between a functionally related sialyltransferase gene ST6GAL1 and Paraprevotella . Given the sensitivity of microbiome analyses to factors including sampling site, feeding status, and analytical framework, independent replication of these findings is important and it is also important to know if the association generalizes across other conditions or is highly specific to certain environments. Here, we performed a replication analysis using stool (not cecal) samples from 174 HS rats that were not fasted prior to collection. Stool samples underwent 16S rRNA gene sequencing, and microbial community structure was analyzed using compositionally aware methods. The rats were genotyped at the top SNP that was associated with Paraprevotella in the Tonnelé et al. (2025) study. The association between genotype and Paraprevotella abundance was tested using a linear mixed model accounting for sex, cohort, and genetic relatedness. We successfully replicated (p=0.015) St6galnac1 - Paraprevotella association. These findings support the robustness of the St6galnac1 - Paraprevotella association across different sampling strategies and experimental conditions.},
}

@article {pmid42999093,
year = {2026},
author = {Doty, CM and Brady, DJ and Barb, JJ and Thompson, SL and Rincon, N and Browning, B and Kelly, DL and Bennett, ME and Elmer, G and Leggio, L and Brandler, BJ and Roche, DJO},
title = {The effect of minocycline on the gut microbiome in individuals with alcohol use disorder and healthy controls.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.09.758026},
pmid = {42999093},
issn = {2692-8205},
abstract = {Alcohol Use Disorder (AUD) is associated with altered gut microbial composition. Yet, many microbiome studies have included AUD populations with co-occurring conditions (e.g., alcohol associated liver disease; ALD), limiting insight into unique contributions of AUD to gut dysbiosis. Further, preclinical studies show that gut microbiome composition can mediate the behavioral effects of minocycline, including alcohol-related and affective behaviors, but no studies have tested these effects in humans with AUD. This study aimed to 1) compare gut microbiome features between healthy controls (HCs) and individuals with AUD, without ALD, and 2) determine the effects of minocycline on the human gut microbiome. We conducted a four-week randomized, double-blind, placebo-controlled trial of minocycline (100-200 mg/day) in adults with AUD (n=31) and HCs (n=26). We collected fecal samples (n=244) at baseline and each weekly visit for 16S rRNA gene sequencing. Alpha diversity (richness and evenness of taxa within a sample) did not differ by diagnostic group, treatment, or time. In contrast, beta diversity (microbiome composition differences between samples) differed between AUD and controls and was shifted by minocycline over time. AUD, vs. controls, was associated with differences in several taxa prevalences, including reduced Dialister and Subdoligranulum and increased Collinsella , Streptococcus , and Phascolarctobacterium . Minocycline, vs. placebo, rapidly and robustly restructured the microbiome, altering numerous taxa, including Lachnospira , Ruminococcaceae , Clostridium sensu stricto , and Christensenellaceae, and metabolic pathways (e.g., ubiquinol biosynthesis and methylphosphonate degradation). AUD is associated with a distinct gut microbial composition, whereas minocycline produces rapid, sustained, diagnosis-independent gut microbiome restructuring, without altering alpha diversity.},
}

@article {pmid42999116,
year = {2026},
author = {Veerus, L and Sun, H and Almet, AA and Levin, ER and Battaje, RR and Dam, VS and Shah, D and Clerk, R and Chang, B and Woortman, MA and Stuckey, JE and Shumaker, MJ and Yin, YS and Kundu, A and Talaue-Weeast, M and Gao, Z and Cardenas, V and Zhang, XS and Nyangahu, DD and Jaspan, HB and Manhart, M and Nie, Q and Barrett, E and Nejsum, LN and Dominguez-Bello, MG and Blaser, MJ and , },
title = {Urea is a dynamic and functional component of mammalian breast milk.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.28.755206},
pmid = {42999116},
issn = {2692-8205},
abstract = {Urea is a constituent of human milk, yet its regulation and interactions with the infant gut microbiome have not been established. Combining three human cohorts, a mouse model, and microbiome analyses, we show that milk urea increases across lactation, is conserved across mammals, and is not explained by maternal serum urea or diet. Instead, we identify lactation-dependent remodeling of mammary urea metabolism and transport, including dynamic epithelial AQP3 localization consistent with regulated urea transfer into milk. Alongside urea, maternal milk and stool provide reservoirs of urea-metabolizing bacteria that help establish the infant "ureabiome", with encoded urea-utilization capacity. This maternal-infant axis is context-dependent: infant formulas provide higher urea levels than human milk, while functional assays show that urea supports both commensal and opportunistic bacteria in a concentration-dependent manner. Together, these findings define a maternal nitrogen axis linking milk urea to infant gut microbiome assembly and function.},
}

@article {pmid42999133,
year = {2026},
author = {Mifflin, KA and Kigerl, KA and Manrique, P and Cyr, A and Medipally, AK and Guan, Z and Gowdy, KM and Popovich, PG},
title = {Oral Bacterial Translocation Promotes Lung Dysbiosis and Infection Risk after Spinal Cord Injury.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.09.758070},
pmid = {42999133},
issn = {2692-8205},
abstract = {Spinal cord injury (SCI) causes systemic pathophysiology that extends beyond the injured spinal cord. Respiratory infections remain a leading cause of death after SCI and can impair neurological recovery, yet the microbial source of these infections remains poorly defined. This study defined the onset and origin of pulmonary dysbiosis after SCI by testing whether commensal bacteria move to the lung from the gut or oral cavity. In a murine model, bacterial culture, 16S rRNA sequencing and source-tracking analyses showed that SCI rapidly increased lung bacterial burden and shifted the pulmonary microbiome toward an oral-like community. Gut-associated bacteria did not measurably reach the lung through lymphatic or vascular routes. Systemic antibiotics commonly used to treat infection failed to reliably reduce post-SCI lung bacterial burden. In contrast, oral and lung-directed antibiotic delivery reduced bacteria linked to post-injury dysbiosis more effectively. These findings identify the oral cavity as a proximal source of lung dysbiosis after SCI, and support route-specific strategies to prevent respiratory infection after SCI.},
}

@article {pmid42999137,
year = {2026},
author = {Nien, TS and Grathwohl, K and Koenig, A and Borries, C and Lu, A and Mallott, EK},
title = {Shifts in the Maternal Gut Microbiome Across Pregnancy are Associated with Energetic Status in Phayre's Leaf Monkeys.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.15.759161},
pmid = {42999137},
issn = {2692-8205},
abstract = {BACKGROUND: During pregnancy, mothers experience physiological changes that support fetal development, including shifts in energy utilization and increasing insulin resistance during late gestation. While these changes benefit the fetus, they can also impose energetic costs that affect the mother's physical condition and metabolic phenotype. Previous studies suggest that the gut microbiome, a key regulator of female metabolism and energy harvest, may play a critical role in mediating these physiological challenges.

RESULTS: In this study, metagenomic sequencing of the gut microbiome of 120 samples revealed dramatic shifts in gut bacterial composition and function associated with pregnancy and lactation in 14 wild Phayre's leaf monkeys, Trachypithecus phayrei crepusculus , from two groups at the Phu Khieo Wildlife Sanctuary, Thailand. Alpha diversity, beta diversity, and taxonomic composition all differed between cycling and the 3 [rd] trimester. Furthermore, bacterial dissimilarity between these states was negatively correlated with postpartum physical condition; that is, mothers whose gut microbiota remained more stable during pregnancy recovered sooner after giving birth. Functional profiling revealed a depletion of pathways involved in purine salvage and glutamate degradation during the 3 [rd] trimester.

CONCLUSION: Overall, our study demonstrates that the gut microbiome undergoes substantial changes during pregnancy, and the stability of these microbial communities predicts postpartum maternal health and potentially influence lifetime reproductive output.},
}

@article {pmid42999170,
year = {2026},
author = {Comrie, JMC and Tan, X and Le, HH and Lee, MT and Richter, A and Thompson, SC and Besler, KR and Johnson, EL},
title = {Dietary omega-3 polyunsaturated fatty acids interact with select gut microbes to produce bioactive metabolites found in infant gut microbiomes.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.10.756005},
pmid = {42999170},
issn = {2692-8205},
abstract = {Gut microbes metabolize nutrients in infant diets, producing compounds that play roles in host health. Long-chain polyunsaturated fatty acids (LCPUFAs) are an important component of infant diets, supporting neurological development and immune regulation. Emerging evidence demonstrates that gut microbes, alongside the host, participate in the metabolism of dietary lipids, highlighting an underexplored avenue for LCPUFA biology. In this work, alkyne-tagged eicosapentaenoic acid (EPA [Alk]) was used to investigate interactions between LCPUFAs and the gut microbiota. Flow cytometry and comparative metabolomics identified gut microbial EPA interactors in the ileum of mice. Further comparative metabolomics analysis identified the conversion of EPA to N -acyl amino acids, including attachment to phenylalanine (EP-Phe) and leucine (EP-Leu). Targeted analysis of ex vivo stool cultures determined that EP-Phe and EP-Leu are produced by gut bacteria. A survey of lipid-relevant infant gut bacteria determined various flow cytometry-confirmed EPA-microbe interactions and identified Enterococcus faecalis, Bacteroides thetaiotaomicron, and Clostridium bifermentans as competent producers of EP-Phe or EP-Leu. Thus, both novel metabolites from diet-derived inputs and microbial producers of these metabolites were identified. Together, this highlights important microbiome-centric consequences of LCPUFA consumption and emphasizes that the gut microbiome may be an important consideration in targeted supplementation strategies.},
}

@article {pmid42999235,
year = {2026},
author = {Niraula, S and Jang, JW and Jung, J and Stirewalt, SL and Alagna, M and Du, J and Staley, C and Seed, P and Green, SJ and Ho, KJ},
title = {Shotgun metagenomic and untargeted metabolomic analysis of gut microbiome associated with peripheral artery disease.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.757428},
pmid = {42999235},
issn = {2692-8205},
abstract = {BACKGROUND: While the human gut microbiome is a potentially important and modifiable risk factor for cardiovascular diseases, the links between the gut microbiome and peripheral artery disease (PAD) and its clinical subgroups (claudication and chronic limb-threatening ischemia; CLTI) are not well understood.

METHODS: We used shotgun metagenomics and untargeted metabolomics to analyze the fecal samples of people with PAD and age- and sex-matched non-PAD controls collected in a cross-sectional manner. We used functional prediction pathways, a network analysis, and weighted gene co-expression network analysis of metagenomic, metabolomics, and clinical data to better understand PAD-associated dysbiosis.

RESULTS: Alpha and beta diversity were similar between the PAD (n=78) and non-PAD (n=20) groups. Differentially abundant species were dominated by those belonging to the Lachnospiraceae, Ruminococcaceae and Enterobacteriaceae families. Fecal butyrate levels were reduced between the non-PAD and PAD groups, but differences were not statistically significant. There was significantly reduced alpha diversity in the samples of the CLTI compared to claudication subgroup. Abundance of multiple butyrate producers were greater in the claudication group compared to CLTI. Network analysis revealed 5 meta-modules, each with specific associations to PAD presentation and metabolomic profiles, and species that are both top module hubs and differentially abundant between groups. Community interconnectedness appears to increase in claudication, followed by community disintegration in CLTI.

CONCLUSIONS: This metagenomic-metabolomic analysis of the gut microbiome of individuals with PAD, highlights the importance of studying functional capacity, diversity, and connectivity between species. Microbial modules may allow an integrative view of the microbial ecology relevant to presence and progression of PAD.},
}

@article {pmid42999269,
year = {2026},
author = {Mannochio-Russo, H and Nelson, MR and Charria-Girón, E and Torres-Ortega, LR and Agongo, J and Gonçalves Nunes, WD and Patan, A and Strobel, M and David, LC and Panitchpakdi, M and Gentry, EC and Caraballo-Rodríguez, AM and Zemlin, J and Kamenik, Z and Acebo, N and Montoya Giraldo, YA and Bauermeister, A and Wang, M and van der Hooft, JJJ and Hagey, LR and Mohanty, I and Dorrestein, PC},
title = {The Evolving Bileome: A Pan-Repository Landscape of Expanded Bile Acid and Related Steroidal Signatures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.10.758218},
pmid = {42999269},
issn = {2692-8205},
abstract = {Bile acids and related steroidal metabolites are among the most studied biomolecules, yet recent work has revealed far greater structural diversity than previously recognized, much of it shaped by the microbiome. We previously introduced a repository-scale bile acid MS/MS library built from queries targeting C24 bile acid fragmentation, limited to Orbitrap Q Exactive datasets within GNPS/MassIVE. Here we announce a major expansion of this library: a bile acid and steroidal MS/MS spectral library assembled across three major metabolomics repositories, now capturing C23, C24 (including alkamine), C26 (C-C bonded aceto derivatives), and C27 bile acids, as well as C28 bile alcohols. The expanded libraries comprise 640,141 unique MS/MS spectra, of which 120,293 (18.8%) match 2,529 reference spectra, leaving most of this steroidal chemical space structurally unassigned. Linked to harmonized pan-repository metadata, the library provides a starting point for classifying MS/MS spectra as likely bile acids or related steroids, with two example analyses illustrated here. This resource allows researchers to flag candidate bile acid and steroidal signatures in their own data for further characterization.},
}

@article {pmid42999290,
year = {2026},
author = {Mitchell, MK and Carty, MA and Snow, NL and Archambault, MT and Budsberg, AE and Carrillo, EV and Vignieri, EE and Older, EA and Rometo, OL and Van de Wal, LE and Floyd, KJ and Baker, LR and Kunkle, CA and Li, J and Ellermann, M},
title = {Cannabinoid receptor 1 activity promotes microbial dysbiosis by stimulating the oxygen-dependent expansion of Enterobacteriaceae.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.10.758071},
pmid = {42999290},
issn = {2692-8205},
abstract = {The endocannabinoid system is comprised of bioactive lipids that signal via cannabinoid receptors, which can modulate barrier and immune functions along the gastrointestinal tract. Clinical studies indicate that endocannabinoid activity is dysregulated in inflammatory bowel diseases. Moreover, an increase in gut endocannabinoids is correlated with microbial dysbiosis in Crohn's disease. Here, we show that endocannabinoid activity promotes metabolic dysfunction within the colonic mucosa, resulting in microbial dysbiosis and exacerbated colitis. Stimulation of the cannabinoid receptor CB1 resulted in the expansion of Enterobacteriaceae within the gut microbiome, a common feature of inflammation-associated dysbiosis. Preceding this microbial change, CB1 activity induced transcriptional signatures of mitochondrial stress and immune activation within the colonic mucosa. This was followed by a reduction in mucosal ATP production and the induction of aerobic respiration genes in luminal Escherichia coli . Genetic inactivation of aerobic respiration in E. coli limited its proliferation, indicating that CB1 activity stimulates oxygen-dependent Enterobacteriaceae growth. In IBD susceptible mice, endocannabinoid activity promoted mucosal infection by an E. coli pathobiont, which corresponded with elevated pro-inflammatory markers. In inflammation resistant mice, acute CB1 stimulation was sufficient to accelerate the infection dynamics of an Enterobacteriaceae pathogen, resulting in exacerbated colitis. Taken together, our data support a model in which endocannabinoid signaling at the CB1 receptor disrupts respiratory metabolism in the colon, compromising the anoxic environment of the lumen that is critical for maintaining aerobically respiring pathogens at low abundance. More broadly, our findings highlight a proinflammatory effect of endocannabinoid activity that can contribute to intestinal disease development.},
}

@article {pmid42999300,
year = {2026},
author = {Krishnavajhala, A and Gingras, MC and Santiago-Rodriguez, TM and Chen, Y and Bandaranaike, D and Bhamidipati, S and Qin, X and Kottapalli, K and Momin, Z and Santhanam, A and Walker, K and Wang, Q and Griffin, SM and Masternak, MM and Ross, MC and Muzny, D and Wu, J and Urquieta, E and Gibbs, RA and Doddapaneni, H},
title = {Microbial Dynamics Across Commercial Spaceflights of Varying Duration.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.29.728784},
pmid = {42999300},
issn = {2692-8205},
abstract = {Spaceflight introduces environmental stressors that can alter human microbiomes and immune responses. We analyzed 259 and 17 biospecimens for microbiome and single-cell studies from n=6 astronauts across two commercial ISS missions: Axiom 2 (10-day mission) and Axiom 3 (21-day mission). Samples included saliva, stool, urine, and body swabs from 10 anatomical sites, profiled via 16S ribosomal RNA (rRNA) gene amplicon sequencing. Gut and oral microbiomes remained stable, while skin-associated communities exhibited transient diversity shifts post-flight. Taxonomic analysis revealed individual and site-specific patterns, as well as from the spaceflight/ISS environment. Cytokine profiling from single-cell data indicated immune activation, with IL-32 and IL-16 transcripts elevated in Axiom 2 and Axiom 3. Microbiome and interleukin correlation analyses found 14 significant associations in Axiom 2 data. These findings provide an integrated view of microbiome individuality. Our study represents a descriptive comparison of two missions, informing strategies for crew health on future long-duration missions.},
}

@article {pmid42999392,
year = {2026},
author = {An, Y and Xia, Y and Sun, J},
title = {Disrupted microbial queuosine biosynthesis contributes to dysbiosis in human inflammatory bowel disease.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.12.26365231},
pmid = {42999392},
abstract = {BACKGROUND AND AIMS: As a microbiome/diet-derived vitamin, queuine (q) is a micronutrient that eukaryotes acquire from microbiota or diet. Vitamin q, the free base form of queuosine (Q), is used for Q-modification of transfer RNA (tRNA). Although tRNA-Q-modification in regulating eukaryotic cell physiology is recognized, the relationship between Q-tRNA-modification and the human microbiome in health and inflammatory bowel diseases (IBD) remains unknown. Which bacteria produce q and how the q-producing bacteria contributing to human health and IBD are not explored. Here, we hypothesize that disrupted microbial Q-biosynthesis contributes to the dysbiosis of human IBD. We performed comprehensive multi-omics integrative analyses using publicly available datasets. Specifically, we re-analyzed publicly available shotgun metagenomic, single-cell RNA sequencing (scRNA-seq), metabolic datasets, and completed meta-analysis.

METHODS: To systematically investigate microbial Q-biosynthesis in healthy individuals and IBD patients, we performed a systematic secondary analysis by integrating 9 publicly available metagenomic datasets, 15 scRNA-seq datasets and one metabolic dataset published prior to 2026. We present a novel secondary bioinformatic reanalysis of sequence outputs mapped to the latest microbial taxonomy, functional pathways and microbial Q-related genes. Longitudinal study of shotgun metagenomics across the human lifespan (3146 samples) enabled taxonomic and functional profiling.

RESULTS: We first identified key q-producing bacteria (e.g., Bacteroides and Alistipes) in healthy populations. We then found that patients with IBD had significantly reducation of q-producing bacteria and a coordinated downregulation of the Q-related pathways, including Q, preQ 0 , de novo guanosine ribonucleotide biosynthesis and de novo guanosine deoxyribonucleotide biosynthesis pathways. This functional impairment was primarily driven by reduced contributions from Bacteroides , Alistipes and Akkermansia . The longitudinal stability of the q-producing bacteria community across the human lifespan (1638 samples). We observed a significant negative correlation between host age and the abundance of q-producing bacteria in patients with UC. Moreover, Queuine tRNA-ribosyltransferase 1 (QTRT1) expression in human intestinal epithelial cells was significantly reduced in patients with IBD compared to healthy controls.

CONCLUSIONS: Our study used multi-omics datasets to define a novel functional dysbiosis characterized by a reduction of microbial Q-biosynthesis in patients with IBD. Vitamin q and its tRNA modification is lesser-recognized in human IBD. Understanding the cellular and organismal mechanisms of this microbiome-dependent micronutrient will advance the prevention of IBD and improve the quality of life of patients with IBD.

Queuine, vitamin q, is a highly conserved hypermodified nucleoside micronutrition could only be acquired from microbiota or diet. It is used for modification of transfer RNA to protein transitional fidelity, but the specific microbial pathways evolved and the relationship with IBD are unclear.

WHAT THIS STUDY ADDS: This study identifies a novel functional dysbiosis in IBD patients characterized by the depletion of q-producing gut bacteria (e.g., Bacteroides and Alistipes) and the downregulated microbial Q biosynthesis pathways, which correlates with host QTRT1 deficiency to potentially drive IBD pathogenesis.

1. Identifies the altered Q-biosynthesis pathway in human IBD. Establishes the "Microbial Q-synthesis-Host tRNA modification" axis as a novel mechanistic link, shifting human IBD microbiome research from taxonomic description to functional epitranscriptomics.Overcomes the inherent biases of traditional meta-analyses through a unified secondary bioinformatic reanalysis, leveraging HMP unified metabolic analysis network 3 (HUMAnN3)-based modeling of 3,000+ samples, to reveal a universal breakdown of the microbial Q-biosynthetic supply chain across all IBD subtypes.Recognize vitamin q as a critical gut-health micronutrient, influencing dietary guidelines and the regulation of functional medical foods for IBD management.},
}

@article {pmid42999460,
year = {2026},
author = {Omeir, K and Ancira, J and Gabrilska, R and Tipton, C and Phillips, N and Wolcott, J and Phillips, CD},
title = {The Structural Genome Shapes the Chronic Wound Microbiome.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.13.26365461},
pmid = {42999460},
abstract = {Recent studies report associations between the patient genome and the chronic wound microbiome, suggesting a causal relationship. Guided by the expectation that larger genomic perturbations are less likely to be neutral, here we study the association of genomic copy number variants (CNVs) with abundances of wound species. Genomic and metagenomic data were collected from 597 patients with chronic wounds at initial clinical visit. Association studies included 831 CNVs and 68 species, implementing a two-cohort design and study-wide significance threshold. There were 47 CNVs (5.7%) associated with 25 species (36.8%); an additional 1,730 associations achieved study-wide significance in one cohort. Associations with haplotype dosage variation dominated significant associations (69.4%) indicating haplotype dosage is important beyond simply locus copy count. Significant co-occurrences between associated and non-associated species, all involving anaerobes, support a model in which the genome selects for certain species that in turn shape the broader microbiome through ecological interactions. Significant CNVs encompassed 66 genes which were functionally overrepresented for several terms, with extracellular matrix (ECM) and ECM-cell interaction terms emphasized. Four collagen and collagen remodeling genes were distributed across four unlinked significant CNVs, a result that strikingly aligns with the previous studies reporting other collagen or ECM component associations. Related, cytoskeletal dynamics are also strongly implicated. Heritability estimates drawing on all available data and controlling for species correlation and patient factors yielded 30 species with significant heritabilities, 24 of which were greater than 20%. These findings extend the genomic basis of the chronic wound microbiome by emphasizing importance of genomic structural variation and suggest a prominent role for variation across ECM-cellular connections as mechanisms defining microbial selection.},
}

@article {pmid42999727,
year = {2026},
author = {Amin, MN},
title = {Microbiome-Derived Metabolites in Multiple Sclerosis: Mechanisms of Immune Regulation and Therapeutic Potential: A Literature Review.},
journal = {Cureus},
volume = {18},
number = {10},
pages = {e117645},
pmid = {42999727},
issn = {2168-8184},
abstract = {Multiple sclerosis (MS) is a chronic autoimmune neuroinflammatory disease characterized by immune dysregulation, demyelination, and neurodegeneration of the central nervous system (CNS). Increasing evidence suggests that gut microbiota and microbiome-derived metabolites play important roles in the pathogenesis and progression of MS by modulating the gut-brain-immune axis. This narrative review examines the possible immunomodulatory effects of microbiome-derived metabolites in MS, with particular emphasis on short-chain fatty acids (SCFAs), tryptophan-derived metabolites, and polyamines, and evaluates their potential therapeutic implications. This review was conducted using the most recent available studies relevant to the topic. The search included PubMed, Google Scholar, and PMC databases. Eligible studies focused on randomized controlled trials, systematic reviews, meta-analyses, observational studies, reviews, and other publications that examined the role of microbiota and its metabolites in MS. The reviewed evidence indicates that MS-associated dysbiosis is accompanied by altered microbial metabolite production, disruption of regulatory T cell (Treg)/T helper 17 (Th17) balance, impaired barrier integrity, and increased neuroinflammation. SCFAs, tryptophan-derived metabolites, and polyamines demonstrate immunoregulatory effects through modulation of T-cell responses, cytokine signaling, and inflammatory pathways. Microbiota-targeted interventions, including probiotics, prebiotics, dietary modulation, and metabolite supplementation, have shown promising immunological and clinical effects. However, methodological heterogeneity, small cohorts, variable interventions, and insufficient long-term clinical validation limit definitive conclusions regarding therapeutic efficacy. Future large-scale longitudinal and multi-omics studies are crucial for clarifying the underlying mechanisms and unlocking microbiota-targeted strategies to manage MS more effectively.},
}

@article {pmid43000087,
year = {2026},
author = {Mei, Z and Dai, DLY and Sifuentes, E and Petersen, C and Turvey, SE},
title = {Microbiome-Targeted Interventions for Pediatric Asthma and Allergic Diseases: Current and Emerging Approaches.},
journal = {Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.anai.2026.10.038},
pmid = {43000087},
issn = {1534-4436},
abstract = {Allergic diseases are among the most common chronic diseases of childhood and remain a major public health challenge. Increasing evidence indicates that the early-life gut microbiome plays a central role in immune maturation, making it an attractive target for allergy prevention. During the first 1000 days of life, interactions between the developing microbiome and the immune system help establish immune tolerance, while disruptions to this process increase the risk of asthma and allergic diseases. Current microbiome-targeted strategies largely focus on optimizing early-life microbial exposures through interventions such as mode of delivery, antibiotic stewardship, breastfeeding, and exposure to diverse environmental microorganisms. These approaches are already incorporated into public health recommendations and promote healthy microbiome development without directly manipulating microbial communities. Newer approaches seek to intervene more precisely through microbial transfer therapies, live biotherapeutic products, prebiotics, postbiotics, and microbial metabolite-based therapies. Although several have shown encouraging preclinical and early clinical results, evidence supporting routine clinical use remains limited. The next generation of microbiome therapeutics is likely to be defined less by changing which microbes are present than by restoring the microbial functions that establish immune tolerance. This conceptual advance is driving the development of increasingly targeted microbiome-based interventions and provides a framework for the next generation of allergy prevention strategies. Translating these mechanistic insights into safe, effective therapies that complement established public health measures represents the next major challenge in preventing asthma and allergic diseases.},
}

@article {pmid43000106,
year = {2026},
author = {Zhao, Y and Chen, Y and Tan, J and Fang, L and Jiang, L},
title = {AI-enabled rumen microbiome engineering for methane mitigation in ruminants.},
journal = {Biotechnology advances},
volume = {94},
number = {},
pages = {109094},
doi = {10.1016/j.biotechadv.2026.109094},
pmid = {43000106},
issn = {1873-1899},
abstract = {Enteric methane from ruminants is a major agricultural source of greenhouse gas emissions, yet durable mitigation remains difficult because methane arises from host-regulated, cross-kingdom microbial networks rather than from methanogens alone. Artificial intelligence (AI) offers a means to integrate methane phenotypes with rumen multi-omics, host genetics, diet, fermentation traits, and environmental data. However, predictive accuracy does not by itself identify causal or controllable targets. Here, rumen methane is framed as a constrained engineering problem in which carbon and reducing equivalents must be redirected while digestibility, animal health, and productivity are preserved. We examine the construction of AI-ready datasets, multimodal prediction, interpretable learning, causal target discovery, and the transition from computational hypotheses to deployable interventions. Particular attention is given to methanogenic pathways, interspecies hydrogen transfer, alternative electron sinks, and context-dependent treatment responses. Demonstrated interventions and prospective engineering strategies include structure-guided inhibitor discovery, redox-routing combinations, live microbial consortia, phage- and enzyme-based control, early-life programming, and adaptive precision deployment. Across these approaches, a complete design-build-test-learn cycle is still needed to connect model outputs with mechanistic assays, rumen simulation, controlled animal studies, and external multi-farm validation. Progress also depends on harmonized phenotypes, leakage-resistant evaluation, transparent uncertainty, standardized reporting, and early consideration of manufacturing, regulation, economics, and life-cycle impacts. AI-enabled rumen microbiome engineering can therefore accelerate methane mitigation only when prediction is linked to causal biology and measurable, persistent performance across diverse ruminant systems.},
}

@article {pmid43000189,
year = {2026},
author = {Morioka, T and Miyaoka, D and Nakatani, S and Kakutani, Y and Miyamoto, S and Nagakura, Y and Uematsu, M and Hirano, T and Yae, H and Yamamoto, M and Sato, N and Fujimoto, K and Emoto, M and Imoto, S and Uematsu, S},
title = {Longitudinal Taxonomic and Predicted Functional Gut Microbiome Responses to Tirzepatide and Semaglutide: An Exploratory Secondary Analysis of the OMDOT-1 Randomized Controlled Trial.},
journal = {Diabetes, obesity & metabolism},
volume = {},
number = {},
pages = {},
doi = {10.1111/dom.71533},
pmid = {43000189},
issn = {1463-1326},
support = {23K15232//Japan Society for the Promotion of Science/ ; JP25K02682//Japan Society for the Promotion of Science/ ; JP25K22560//Japan Society for the Promotion of Science/ ; JP26H02419//Japan Society for the Promotion of Science/ ; JP26K19344//Japan Society for the Promotion of Science/ ; JP26ae0121040//Japan Agency for Medical Research and Development/ ; JP26ae0121048//Japan Agency for Medical Research and Development/ ; },
abstract = {AIMS: Glucagon-like peptide-1-based therapies improve metabolic outcomes, but longitudinal gut microbiome dynamics remain poorly characterized. We compared taxonomic and predicted functional microbiome responses to tirzepatide and semaglutide in Type 2 diabetes.

MATERIALS AND METHODS: This exploratory secondary analysis included 36 participants from a randomized controlled trial comparing tirzepatide, semaglutide and conventional treatment. Faecal samples were collected at five time points over 16 weeks and analyzed by 16S rRNA gene sequencing. Genus-level features were screened using MaAsLin2, and candidate genera were further evaluated using longitudinal mixed-effects models. Predicted microbial functions were inferred using PICRUSt2 and analyzed using MaAsLin2. Primary analyses were adjusted for baseline body mass index, with exploratory sensitivity analyses additionally adjusted for changes in body weight and haemoglobin A1c.

RESULTS: No significant between-group differences in beta diversity were observed. Alpha diversity increased predominantly in the tirzepatide group, with a significant time-by-treatment interaction versus control. Longitudinal trajectories relative to the control group differed for several genera, including Romboutsia_B, Barnesiella and Ruminococcus_E with both treatments and Vescimonas with tirzepatide (q < 0.05). Across 2106 predicted EC features, longitudinal effects were positively correlated between tirzepatide and semaglutide (67.1% concordant direction; Pearson r = 0.450, p < 0.001). Treatment-versus-control analyses identified predicted functional changes involving energy and carbohydrate metabolism.

CONCLUSIONS: Tirzepatide and semaglutide were associated with partially distinct taxonomic changes, accompanied by broadly similar predicted functional patterns. These longitudinal findings complement, while remaining distinct from, Week-16 shotgun metagenomic endpoint analyses.

TRIAL REGISTRATION: Japan Registry of Clinical Trials (jRCT), jRCT1051240017.},
}

@article {pmid43000446,
year = {2026},
author = {Zhuo, Q and Fu, K and Liu, Z and Zhang, H},
title = {Bacillus subtilis attenuates acetaminophen-induced liver injury and preserves gut-liver homeostasis in mice.},
journal = {Cell communication and signaling : CCS},
volume = {24},
number = {1},
pages = {},
pmid = {43000446},
issn = {1478-811X},
support = {81802964//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Bacillus subtilis/physiology ; *Acetaminophen/adverse effects ; *Chemical and Drug Induced Liver Injury/pathology/metabolism/microbiology ; *Liver/pathology/metabolism/drug effects ; Mice ; Male ; *Homeostasis/drug effects ; *Probiotics/pharmacology ; Mice, Inbred C57BL ; Intestines ; },
abstract = {Acetaminophen (APAP) overdose produces an early oxidative insult followed by sterile inflammation and tissue repair, but whether probiotic interventions can influence these distinct phases remains unclear. Here, we evaluated the effects of Bacillus subtilis on APAP-induced liver injury in mice. B. subtilis pretreatment reduced serum aminotransferases and hepatic necrosis, restored the hepatic GSH/GSSG ratio, and decreased cellular ROS and p-JNK level at 24 h. When B. subtilis treatment was initiated after APAP and continued daily, it did not significantly reduce liver injury at 48 h but lowered serum aminotransferases and residual hepatic necrosis at days 5 and 7, consistent with a later recovery-associated benefit. B. subtilis pretreatment reduced the frequencies of Ly-6G[+] neutrophils and total myeloid cells during acute injury, increased the proportion of TIM4[+] Kupffer cells during recovery, and shifted serum cytokines toward a less inflammatory profile. In parallel, B. subtilis preserved colonic morphology and occludin/ZO-1 expression and lowered circulating LPS. Recovery-stage transcriptomic and microbiome analyses associated B. subtilis with antioxidant and metabolic programs and altered microbial community structure. Metabolomic analysis identified candidate metabolites elevated in B. subtilis-treated mice; among these, histidine and acetyl-L-carnitine were selected for functional testing and provided partial biochemical protection, whereas only live B. subtilis reproduced the combined hepatic and intestinal effects. These findings show that viable B. subtilis limits acute APAP hepatotoxicity and supports recovery while preserving intestinal barrier integrity.},
}

Animals
*Bacillus subtilis/physiology
*Acetaminophen/adverse effects
*Chemical and Drug Induced Liver Injury/pathology/metabolism/microbiology
*Liver/pathology/metabolism/drug effects
Mice
Male
*Homeostasis/drug effects
*Probiotics/pharmacology
Mice, Inbred C57BL
Intestines

@article {pmid42996360,
year = {2026},
author = {Holsinger, RMD},
title = {Editorial: Decoding the gut-brain axis: implications for neurodegenerative disease therapies.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {2015896},
doi = {10.3389/fnagi.2026.2015896},
pmid = {42996360},
issn = {1663-4365},
}

@article {pmid42996471,
year = {2026},
author = {Shao, H and Li, X and Miao, X and Tang, L and Gu, Y and Qin, Z and Han, J and Li, J and Wang, Q and Yang, W and Chen, H and Wu, J},
title = {Characterization of lower-airway microbial communities in pulmonary tuberculosis by BALF metagenomic sequencing.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1938581},
pmid = {42996471},
issn = {2235-2988},
mesh = {Humans ; *Bronchoalveolar Lavage Fluid/microbiology ; *Tuberculosis, Pulmonary/microbiology ; *Metagenomics/methods ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Female ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Middle Aged ; Bronchoscopy ; *Bacteria/classification/genetics/isolation & purification ; Metagenome ; Adult ; },
abstract = {OBJECTIVE: Pulmonary tuberculosis (PTB) is an infectious disease caused by the Mycobacterium tuberculosis complex (MTBC). This study aimed to characterize the lower-airway microbiome in patients with PTB and compare it with that of patients without PTB (Non-PTB) undergoing bronchoscopy for pulmonary disease, in order to describe differences in microbial composition between the two groups and improve our understanding of pulmonary microbial ecology in tuberculosis.

METHODS: We performed metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) from 75 patients (38 PTB, 37 Non-PTB). Microbial diversity, composition, and differential taxa were analyzed using standard bioinformatics tools.

RESULTS: PTB samples showed higher Shannon and Simpson indices, whereas Richness did not differ significantly between groups. Beta diversity analyses revealed modest but statistically detectable differences in microbial community composition between PTB and Non-PTB samples. The PTB group showed higher relative abundances of MTBC and several oral-associated taxa (e.g., Prevotella and Fusobacterium), whereas Non-PTB samples showed higher relative abundances of taxa including Pseudomonas aeruginosa and Aspergillus fumigatus.

CONCLUSION: This BALF metagenomic study characterized lower-airway microbial features in patients with PTB and identified differences in microbial community composition and structure between PTB and patients with heterogeneous Non-PTB pulmonary diseases.},
}

Humans
*Bronchoalveolar Lavage Fluid/microbiology
*Tuberculosis, Pulmonary/microbiology
*Metagenomics/methods
*Microbiota
High-Throughput Nucleotide Sequencing
Female
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Middle Aged
Bronchoscopy
*Bacteria/classification/genetics/isolation & purification
Metagenome
Adult

@article {pmid42996472,
year = {2026},
author = {Zhang, X and Wang, H and Xing, J and Zhao, H and Liu, Y and Jiao, J},
title = {Microecological-metabolic links along the brain-gut-muscle axis in Tuina analgesia from the perspectives of gut metagenomics and untargeted metabolomics.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1957609},
pmid = {42996472},
issn = {1664-302X},
abstract = {Chronic pain involves multilevel processes including central sensitization, peripheral tissue abnormalities, neuroimmune responses, metabolic alterations, and changes in gut microecology. Tuina and related manual therapies can influence local soft-tissue status, peripheral sensory input, autonomic activity, inflammatory responses, and muscle metabolism, whereas the links between their distal systemic effects and gut microecology remain insufficiently characterized. The brain, gut, and skeletal muscle can interact through autonomic pathways, immune-inflammatory signaling, circulating metabolites, myokines, and other distal signals, providing a biological context for analyzing cross-organ changes related to Tuina analgesia. A limited number of studies have reported changes in gut microbiota after Tuina, massage, or combined manual interventions; however, direct evidence continuously linking mechanical stimulation, microbial function, metabolic signaling, and pain improvement remains limited. Gut metagenomics extends analysis beyond species composition to strains, functional genes, and metabolic pathway potential, whereas untargeted metabolomics captures metabolic changes jointly shaped by the host and microbiota. Short-chain fatty acids, bile acids, tryptophan derivatives, and molecules related to lipid and energy metabolism have shown functional associations with neuroimmune regulation, sensory neural activity, and pain sensitization in different pain models. Myokines, metabolites, and extracellular vesicle signals derived from skeletal muscle also provide a possible biological basis for bidirectional gut-muscle communication. Nevertheless, most of these mechanisms originate from studies of pain, the microbiome, or exercise physiology and cannot be directly equated with mechanisms of Tuina analgesia. Integrated metagenomic and metabolomic analyses can identify candidate links involving microbial functions, metabolic alterations, host responses, and pain phenotypes, thereby narrowing the scope of subsequent functional validation. Their interpretation remains influenced by Tuina stimulation parameters, diet, gut transit, medication use, circadian rhythms, and other host factors. Standardization of the intervention, longitudinal multi-omics observation, targeted quantification, functional experiments, and cross-center replication will help clarify the temporal relationships and functional significance of these changes. Microecological-metabolic links across the brain, gut, and skeletal muscle can therefore serve as a cross-organ framework for investigating the systemic effects of Tuina analgesia, although specific pathways and their clinical predictive value still require direct experimental and prospective validation.},
}

@article {pmid42996507,
year = {2026},
author = {Zhang, P and Zhang, X and Ji, C and Hu, W},
title = {Chinese herbal medicine for recurrent urinary tract infection: formulation-specific clinical evidence, experimental pharmacology, and unresolved recurrence mechanisms.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1950004},
pmid = {42996507},
issn = {1663-9812},
abstract = {Chinese herbal medicine (CHM) is used for recurrent or chronic urinary symptoms within the traditional category of dysuria, often through stage-specific treatment during symptomatic and remission phases. Whether defined CHM preparations prevent recurrent bacterial cystitis or modify recurrence biology remains uncertain. The aim of this study is to critically evaluate formulation-specific clinical evidence for CHM in women with recurrent urinary tract infection (rUTI) and determine whether reported benefits are connected to recurrence biology.

MATERIALS AND METHODS: Structured searches of PubMed, China National Knowledge Infrastructure, and Wanfang Data were closed on 13 July 2026. After within-batch screening and cross-source reconciliation, 103 reports were linked into 96 study or unresolved-report clusters. Clusters were classified by directness, and clinical confidence was appraised using allocation, participant flow, recurrence ascertainment, denominator integrity, comparator, intervention identity, safety reporting, internal consistency, and report independence.

RESULTS: Ten core clusters directly addressed prospective recurrence or suppressive treatment, but every comparative estimate was of very low confidence. Reported signals were formulation-specific and were limited by attrition, responder-conditioned denominators, active comparators, co-interventions, poorly defined recurrence, internal numerical inconsistencies, or report linkage. Botanical identity and study-batch chemistry were usually inadequate. Experimental studies supported anti-adhesion, virulence-modulating, anti-inflammatory, immune, and urothelial plausibility, including chemically characterized Persicaria capitata extract and more specific Caveolin-1 evidence for purified cynaroside, but predominantly used acute or pretreatment models. No microbiome or biomarker study evaluated clinical mediation.

CONCLUSION: Current evidence is inconclusive rather than uniformly negative and supports cautious hypothesis generation for specific preparations, not a class-wide efficacy or safety claim. No clinical study demonstrates that CHM reduces recurrence by clearing persistent uropathogens, interrupting gut-bladder or vaginal transmission, restoring microbial ecology, or repairing the urothelial barrier. Reproducible products, intention-to-treat recurrence trials, longitudinal strain-resolved sampling, and prespecified mediation analyses are required.},
}

@article {pmid42996510,
year = {2026},
author = {Zhong, X and Wu, H and Na, HK},
title = {Dietary Regulation of the Tumor Immune Microenvironment in Cancer Immunotherapy.},
journal = {Journal of cancer prevention},
volume = {31},
number = {4},
pages = {195-213},
pmid = {42996510},
issn = {2288-3649},
abstract = {Cancer progression is driven by complex interaction among malignant cells, stromal components, and tumor-infiltrating immune cells, which together define the tumor immune microenvironment (TIME). Tumor cells evade immune surveillance by impairing the cytotoxic CD8[+] T-cell function and promoting immunosuppressive cell populations including regulatory T cells, tumor-associated macrophages, and myeloid-derived suppressor cells. Although immune checkpoint blockade and adoptive T-cell therapy have advanced cancer treatment, their clinical efficacy remains limited by therapeutic resistance, heterogenous responses, and treatment-related toxicities. Dietary factors have emerged as potential modulators of antitumor immunity through their effects on immune cell metabolism, inflammatory signaling, and the gut microbiota. In this review, we summarize the mechanisms underlying immunosuppression within the TIME and discuss how macronutrients, micronutrients, food-derived bioactive compounds, and dietary patterns regulate immune cell function and antitumor immune responses. We further highlight the potential of dietary modulation to improve immunotherapy outcomes while critically evaluating current preclinical and clinical evidence. Finally, we discuss the challenges associated with translating these findings into clinical practice, including bioavailability, context-dependent effects, and the need for well-designed clinical trials. A better understanding of diet-mediated immune regulation may provide new opportunities for developing complementary strategies to enhance cancer immunotherapy.},
}

@article {pmid42996652,
year = {2026},
author = {Rowe, JC and Winston, JA},
title = {Bile acid dysmetabolism and microbial dysbiosis coincide with Clostridioides difficile infection in pediatric inflammatory bowel disease.},
journal = {Npj gut and liver},
volume = {3},
number = {1},
pages = {35},
pmid = {42996652},
issn = {3004-9806},
support = {K08 AI153550/AI/NIAID NIH HHS/United States ; },
abstract = {Pediatric inflammatory bowel disease (IBD) patients are at increased risk for Clostridioides difficile infection. This review highlights bile acid dysmetabolism, driven by gut microbiota dysbiosis and reduced microbial production of secondary bile acids, as a key factor linking pediatric IBD to increased CDI susceptibility. We examine interactions among IBD, dysbiosis, bile acid metabolism, and C. difficile, and discuss emerging microbiome-based interventions aimed at restoring bile acid homeostasis.},
}

@article {pmid42996672,
year = {2026},
author = {Adamu Bukari, AR and Opulente, DA and Hittinger, CT and d'Enfert, C and Cuomo, CA and Gerstein, AC},
title = {Linking geography, isolation source, and genomic diversity in a global Candida albicans phylogeny.},
journal = {Npj fungal science},
volume = {1},
number = {1},
pages = {7},
pmid = {42996672},
issn = {3091-3896},
support = {U19 AI110818/AI/NIAID NIH HHS/United States ; },
abstract = {Candida albicans is a common commensal species in the human microbiome at multiple sites and an opportunistic pathogen. Previous phylogenomic analyses identified major clades but often relied on imprecise genomic methods, limited geographic and ecological sampling, and non-standardized strategies for phylogenetic resolution. Here, we address these gaps by reconstructing a whole-genome phylogeny to examine how geography and site of isolation contribute to phylogenetic structure in C. albicans. We analyzed phased genomes from 945 global isolates obtained across diverse clinical and ecological contexts and applied an agnostic, threshold-based clustering approach to systematically define cluster boundaries and quantify intraspecific genomic features. Our analyses preserved previously defined major clusters while identifying six novel clusters, predominantly composed of highly admixed Asian isolates. Although geographic origin and isolation source were each significantly associated with cluster membership, these associations were confounded because isolates from specific regions were disproportionately derived from particular sources. However, an analysis of environmental isolates alongside a diverse strain collection from Winnipeg, Canada, highlights the potential for frequent local transmission. More than 95% of isolates were heterozygous at the mating-type locus, while aneuploidy was present in 8% of isolates distributed across the phylogeny. Analysis of the AGO1 PAZ domain involved in RNAi interference identified both known and novel RNAi variants, predominantly in a heterozygous state. Intra-host analysis of isolates from 95 individuals revealed predominantly clonal colonization, though fourteen individuals harbored isolates from different clusters. Together, these findings refine the phylogenetic structure of C. albicans and provide insights into genomic plasticity and strain transmission in this common fungal species.},
}

@article {pmid42996839,
year = {2026},
author = {Zaniboni, A},
title = {Management of diarrhea in patients receiving liposomal irinotecan-based regimens: a narrative review of mechanisms, clinical impact, and evidence-based strategies.},
journal = {Journal of gastrointestinal oncology},
volume = {17},
number = {5},
pages = {325},
pmid = {42996839},
issn = {2078-6891},
abstract = {BACKGROUND AND OBJECTIVE: Liposomal irinotecan (nal-IRI) in combination with 5-fluorouracil and leucovorin (5-FU/LV) represents the standard second-line treatment for metastatic pancreatic ductal adenocarcinoma (mPDAC) following progression on gemcitabine-based therapy. Despite its demonstrated survival benefit, diarrhea remains a clinically significant toxicity that can compromise dose intensity, treatment adherence, and quality of life. This review provides a comprehensive and updated overview of the pathophysiology, incidence, and evidence-based management of diarrhea associated with nal-IRI-based regimens.

METHODS: A structured narrative review of the available literature was performed, including prospective randomized trials, supportive care guidelines, pharmacogenomic data, and emerging translational evidence. Given the heterogeneity of study designs and the limited number of nal-IRI-specific supportive care trials, a formal meta-analysis was not feasible.

KEY CONTENT AND FINDINGS: Diarrhea associated with nal-IRI is mechanistically complex, encompassing acute cholinergic and delayed secretory components mediated by SN-38-induced mucosal injury and enterohepatic recirculation. Grade 3-4 diarrhea occurs in approximately 13-20% of patients across major pancreatic cancer trials. Evidence-based management strategies are presented, including pharmacologic interventions (atropine, loperamide, octreotide, fluoroquinolones), supportive care, and dose modification protocols. Emerging approaches-including gut microbiome modulation, beta-glucuronidase inhibitors, and novel antisecretory agents-are also reviewed.

CONCLUSIONS: A multidisciplinary, proactive management approach-beginning before the first nal-IRI dose-is essential to minimize diarrhea-related morbidity and optimize treatment outcomes. Integration of pharmacogenomic data and emerging biomarkers-particularly UGT1A1*28 genotyping and gut microbiome β-glucuronidase activity profiling-may further individualize risk stratification and management in this patient population.},
}

@article {pmid42996978,
year = {2026},
author = {Sun, Y and Hong, Z and Guo, Y and Cui, H and Jiang, Y and Yu, Q},
title = {The mucosal immune microenvironment in chronic pharyngitis: epithelial barrier dysfunction, inflammatory persistence, and therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {2000898},
pmid = {42996978},
issn = {1664-3224},
mesh = {Humans ; *Pharyngitis/immunology/therapy/microbiology ; Chronic Disease ; Animals ; *Immunity, Mucosal ; *Cellular Microenvironment/immunology ; Inflammation/immunology ; Immunity, Innate ; Adaptive Immunity ; Microbiota ; },
abstract = {Chronic pharyngitis is a clinically heterogeneous condition in which persistent throat symptoms, visible mucosal abnormalities, and underlying biological processes do not necessarily coincide. This critical narrative review synthesizes evidence from human chronic pharyngitis, experimental injury models, adjacent upper-airway disorders, and other mucosal systems to examine how epithelial barrier function, innate and adaptive immunity, microbial ecology, sensory signaling, and tissue repair may contribute to disease persistence. Experimental studies identify epithelial injury and activation of shared inflammatory and stress-response pathways, while human observations highlight substantial variation in anatomical site, microbial findings, immune organization, and treatment response. Adaptive immune responses appear strongly context dependent; microbial community changes are most informative when linked to organism viability, metabolite production, host sensing, or colonization resistance; and sensory pathways may contribute to symptoms partly independently of measurable inflammation. We propose that persistent disease can arise through three overlapping routes: continued exposure, durable alteration of tissue responsiveness, and incomplete resolution or repair, with microbial and sensory processes acting as modifiers. This framework separates symptom improvement, biological target engagement, and durable restoration of tissue function as distinct therapeutic outcomes. Future studies should prioritize anatomically precise longitudinal cohorts, site-resolved single-cell and spatial profiling, functional perturbation in primary pharyngeal systems, and mechanism-informed trials with follow-up after treatment withdrawal. By linking clinical presentation to local biological function and recovery trajectories, chronic pharyngitis may be reclassified into reproducible biological subgroups that support more precise mechanistic investigation and treatment.},
}

Humans
*Pharyngitis/immunology/therapy/microbiology
Chronic Disease
Animals
*Immunity, Mucosal
*Cellular Microenvironment/immunology
Inflammation/immunology
Immunity, Innate
Adaptive Immunity
Microbiota

@article {pmid42997004,
year = {2026},
author = {Cheng, YJ and Tao, MP and Qian, K and Ye, W},
title = {Reprogramming the gut-brain axis in neurodegeneration: comparative microbiome, metabolite, immunometabolic, polyphenol, probiotic, and epigenetic mechanisms in Alzheimer's and Parkinson's diseases.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1865514},
pmid = {42997004},
issn = {1663-4365},
abstract = {The gut-brain axis has emerged as a central mechanistic framework linking dietary bioactives, microbial ecology, and neurodegenerative disease progression. Similar microbiome-related mechanisms have also been implicated in colorectal cancer, suggesting potential shared links between microbial dysbiosis, inflammation, and disease progression. This study synthesizes preclinical evidence examining how polyphenols, polyphenol-derived compounds, and advanced delivery systems, including nanoparticles and synbiotics, modulate Alzheimer's disease (AD) and Parkinson's disease (PD) through microbiome-dependent mechanisms. Evidence from transgenic mice, toxin-induced rodent models, and Drosophila systems was compared across microbiome alterations, microbial metabolites, signaling pathways, epigenetic regulation, and functional outcomes. Across AD and PD models, dietary bioactives consistently promoted restoration of gut microbial homeostasis, characterized by enrichment of beneficial taxa and reduction of dysbiosis-associated microorganisms. These changes were accompanied by alterations in microbial metabolites, particularly short-chain fatty acids (SCFAs), tryptophan-derived metabolites, and lipid-associated signaling molecules. These metabolites provide functional links between microbial ecology and CNS physiology and may regulate epigenetic processes, including histone acetylation, DNA methylation, chromatin remodeling, and non-coding RNA activity. Despite substantial upstream convergence, downstream effects showed disease-specific patterns. In AD models, microbiome modulation predominantly influenced metabolic, amyloidogenic, and neurotrophic pathways, including AKT/GSK3β, NRF2, NF-κB, and BDNF-associated signaling, contributing to reduced amyloid-β deposition, attenuated tau pathology, and improved cognitive outcomes. In PD models, greater emphasis was placed on inflammatory, oxidative, and mitochondrial pathways involving SIRT1/NRF2, TLR4/MyD88/NF-κB, inflammasome signaling, and neuronal survival mechanisms, resulting in reduced neuroinflammation and preservation of dopaminergic neurons and motor function. Epigenetic regulation represents an additional convergence layer through which microbial metabolites and polyphenols may influence inflammatory, metabolic, mitochondrial, and neuronal gene programs in both disorders. Nanoparticle-based delivery systems enhanced bioavailability, tissue targeting, and microbiome-related effects, whereas synbiotic strategies reinforced microbial and metabolic homeostasis. Collectively, these findings support a microbiome-metabolite-epigenome-brain framework in which dietary bioactives modulate neurodegeneration through interconnected microbial, metabolic, immune, redox, mitochondrial, and epigenetic pathways. This framework provides a mechanistic basis for developing disease-tailored and precision-oriented gut-brain interventions for AD and PD.},
}

@article {pmid42997201,
year = {2026},
author = {Li, Z and Yang, Y and Liu, B and Sun, J and Tang, X and Yang, Y},
title = {Clear aligner interface properties, oral microbial ecology, and strategies for biofilm control and caries-risk mitigation: a scoping review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1951083},
pmid = {42997201},
issn = {2235-2988},
mesh = {*Biofilms/growth & development ; Humans ; *Dental Caries/prevention & control/microbiology ; *Microbiota ; *Mouth/microbiology ; Saliva/microbiology ; Bacterial Adhesion ; },
abstract = {BACKGROUND: Clear aligners create an aligner-tooth interface that may retain saliva, microorganisms, and dietary substrates. Evidence linking interface properties, oral microecological responses, and preventive interventions remains fragmented.

OBJECTIVE: To map and synthesize evidence on clear aligner interface properties and microbial adhesion, oral microbial ecology during clear aligner wear, and strategies for biofilm control and caries-risk mitigation.

METHODS: Following Joanna Briggs Institute methodology and PRISMA-ScR guidance, PubMed, Embase, and Web of Science Core Collection were searched from inception to August 31, 2026, without language restrictions. Backward and forward citation searching supplemented database searches. Original clinical, in vitro, and ex vivo studies involving active clear aligner treatment, associated materials or interfaces, or clear-aligner-specific interventions were eligible when they reported microbial, biofilm, microbiome, metabolomic, caries-related, or mineral outcomes. Two reviewers independently screened records; two authors charted and verified data. Findings were synthesized descriptively within three evidence domains.

RESULTS: Of 988 records, 132 reports were included. Because reports could contribute to more than one domain, 62 informed interface properties and microbial adhesion, 47 oral microbial ecology during wear, and 76 biofilm control and caries-risk mitigation. No single polymer, manufacturing method, or surface parameter consistently predicted microbial adhesion or biofilm formation. Outcomes reflected interactions among material characteristics, local topography, salivary conditioning, aging and exposure, microbial species, and experimental models. Clinical microbial responses were compartment- and time-dependent. Salivary and tooth-associated communities often remained relatively stable at the community level, whereas the inner aligner surface sometimes exhibited localized taxonomic, functional, metabolic, and pH-related changes. Investigated interventions included cleaning, antimicrobial and antifouling interface modifications, anticaries and remineralizing approaches, probiotics, and environment-responsive systems. Although many strategies reduced microbial burden, biofilm-related outcomes, acidogenicity, or mineral loss under tested conditions, evidence was predominantly short-term and preclinical. Assessments of durability, material performance, and safety were heterogeneous.

CONCLUSIONS: Clear aligner-microbiota interactions appear context-dependent rather than uniformly favorable or unfavorable. Evidence neither establishes causal relationships between interface or microecological changes and clinical disease nor identifies a universally superior intervention. More standardized, clinically representative evidence may clarify their clinical relevance and inform preventive management during clear aligner treatment.},
}

*Biofilms/growth & development
Humans
*Dental Caries/prevention & control/microbiology
*Microbiota
*Mouth/microbiology
Saliva/microbiology
Bacterial Adhesion

@article {pmid42997212,
year = {2026},
author = {Khan, FZA and Ali, SA},
title = {Maternal iron deficiency, preterm birth, and disrupted microbial inheritance: a proposed double-hit hypothesis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1953925},
pmid = {42997212},
issn = {2235-2988},
mesh = {Humans ; Female ; *Premature Birth/microbiology/etiology ; Vagina/microbiology ; Infant, Newborn ; Pregnancy ; Dysbiosis/microbiology ; Milk, Human/microbiology ; *Microbiota ; *Iron Deficiencies ; Iron ; Gastrointestinal Microbiome ; *Anemia, Iron-Deficiency/complications ; },
abstract = {The maternal microbiome is the infant's primary microbial inheritance, transmitted mainly through the maternal gut, vaginal delivery, breast milk, and skin-to-skin contact. Maternal iron deficiency (ID), with anemia, is a common and modifiable nutritional condition associated with impaired immune function and increased preterm birth (PTB) risk, whereas evidence for ID without anemia remains limited. It may influence maternal microbial ecology; however, its potential effect on maternal-to-infant microbial transmission remains unexplored. This review, conducted across PubMed, Embase, and Web of Science (January 2000-June 2026), proposes a double-hit hypothesis defined by the source and biological context of disruption rather than by a strictly temporal sequence. The first hit comprises potentially altered maternal-origin microbial and immunologic inputs from the vaginal, gut, and breast milk ecosystems; the second hit comprises PTB and neonatal intensive care (NICU)-associated disruption of early microbial succession. Human evidence directly linking ID to vaginal dysbiosis is limited to a single study, evidence relating maternal iron status to milk lactoferrin is inconsistent, and the contribution of vaginal communities to persistent infant gut colonization remains uncertain whereas vaginal exposure may have transient ecological or immunologic effects. No study has simultaneously evaluated maternal iron biomarkers, vaginal community state type (CST), breast milk composition, maternal gut microbiome and longitudinal infant gut microbiota. The proposed framework is therefore hypothesis-generating and identifies testable pathways through which maternal ID may alter maternal microbial and immunologic inputs, while also being associated with an increased risk of PTB. PTB, together with the resulting prematurity-related vulnerability and subsequent postnatal exposures, may further disrupt early infant microbiome development.},
}

Humans
Female
*Premature Birth/microbiology/etiology
Vagina/microbiology
Infant, Newborn
Pregnancy
Dysbiosis/microbiology
Milk, Human/microbiology
*Microbiota
*Iron Deficiencies
Iron
Gastrointestinal Microbiome
*Anemia, Iron-Deficiency/complications

@article {pmid42997231,
year = {2026},
author = {He, X and Zhang, B and Zhao, E and Fang, Y and Liu, J and Zhu, Y and Xu, H and Zhao, Q and Song, X and Wang, T and Xu, H and Huang, W},
title = {Exposure to Size-Fractioned Ambient Particles Associated with Alterations in Gut Microbiome and Pro-Atherosclerotic Biomarkers in Young Adults.},
journal = {Environmental health perspectives},
volume = {134},
number = {7},
pages = {904-922},
pmid = {42997231},
issn = {1552-9924},
mesh = {Humans ; Biomarkers ; *Gastrointestinal Microbiome/drug effects ; *Particulate Matter/adverse effects ; Particle Size ; Young Adult ; Male ; Female ; *Air Pollutants/adverse effects ; *Environmental Exposure/adverse effects ; Longitudinal Studies ; Beijing ; Adult ; *Atherosclerosis/epidemiology ; Feces ; },
abstract = {Background: Ambient fine and ultrafine particles are linked to the progression of atherosclerotic cardiovascular diseases, wherein gut microbiome may play a critical role. However, the underlying mechanisms and relevant metabolic pathways are not yet fully understood. Objectives: To identify the features and metabolic pathways of gut microbiome, and to explore their potential roles in the pro-inflammatory and pro-atherosclerotic effects of particles in size ranges of 5-560 nm (measured as number concentration, PNC5-560). Methods: We conducted a longitudinal panel study of 152 young adults in Beijing, China, with four monthly clinical examinations between September 2019 and January 2020. Gut microbiome, fecal metabolome, and circulating pro-inflammatory and pro-atherosclerotic biomarkers were measured. Linear mixed-effects models were used to examine the associations linking short-term PNC5-560 exposure to health indicators. We further evaluated whether gut microbiota could mediate changes in these biomarkers and identified the underlying metabolic pathways. Results: Major sources of PNC5-560 in the study area were identified as diesel vehicle emissions (37.9%), gasoline vehicle emissions (39.4%), nucleation (9.2%), and secondary aerosols (11.9%). Per interquartile range increment in PNC5-560 over the preceding 7 days was associated with significant elevations in circulating pro-inflammatory and pro-atherosclerotic biomarkers, with effect estimates ranging from 2.1% (95% CI: 0.4%, 3.8%) to 198.6% (95% CI: 29.3%, 365.8%). PNC5-560 exposure was also associated with decreased gut microbial α-diversity (e.g., Shannon, Simpson, and Chao1) and altered taxonomic composition. Several microbial species (e.g., Solibaculum mannosilyticum, Bacteroides stercoris, and Bifidobacterium longum) were identified as potential mediators of the effects of PNC5-560 on pro-inflammatory and pro-atherosclerotic responses, with mediation proportions up to 9.8% (95% CI: 0.8, 38.3) and 4.8% (95% CI: 0.09, 22.5), respectively. Functional analyses further revealed that these mediating effects involved perturbations in nucleotide and amino acid metabolism pathways. Conclusions: This study provides evidence suggesting that gut microbiome may regulate nucleotide and amino acid metabolism, thereby partially mediating the detrimental cardiovascular effects of size-fractioned ambient particles.},
}

Humans
Biomarkers
*Gastrointestinal Microbiome/drug effects
*Particulate Matter/adverse effects
Particle Size
Young Adult
Male
Female
*Air Pollutants/adverse effects
*Environmental Exposure/adverse effects
Longitudinal Studies
Beijing
Adult
*Atherosclerosis/epidemiology
Feces

@article {pmid42997375,
year = {2026},
author = {Bai, Y and Yu, Y and Huang, X and Yang, X and Yu, R and Xiang, Q},
title = {Effects of probiotic or synbiotic supplementation on glycolipid metabolism in patients with coronary heart disease: a systematic review and meta-analysis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1877366},
pmid = {42997375},
issn = {1664-302X},
abstract = {OBJECTIVE: This systematic review and meta-analysis, combined with trial sequential analysis (TSA), evaluated the effects of probiotic/synbiotic supplementation on glycolipid metabolism in patients with coronary heart disease (CHD).

METHODS: Randomized controlled trials published up to May 1, 2026, were systematically searched across major databases, including PubMed, Embase, Cochrane Library, Web of Science, MEDLINE, and ClinicalTrials.gov. Pooled analyses were performed using Review Manager 5.3, and TSA was conducted to assess the conclusiveness of evidence. Mean difference (MD) and risk ratio (RR) were calculated for continuous and dichotomous outcomes, respectively.

RESULTS: Six trials involving 296 participants were included. Probiotic/synbiotic supplementation was associated with a reduction in fasting blood glucose (FBG) (MD - 19.25 mg/dL, 95% CI -32.28 to -6.22, p = 0.004) and an increase in high-density lipoprotein cholesterol (HDL-C) (MD 3.70 mg/dL, 95% CI 1.65 to 5.74, p = 0.0004) based on four studies involving 192 participants. No significant effects were observed on low-density lipoprotein cholesterol, very low-density lipoprotein cholesterol, total cholesterol, triglycerides, insulin, homeostasis model assessment of insulin resistance, quantitative insulin sensitivity check index, systolic blood pressure, or diastolic blood pressure (p ≥ 0.05). Although adverse event rates did not differ significantly (p ≥ 0.05), safety evidence was limited by few events and a wide confidence interval. TSA showed that the cumulative evidence for both HDL-C and FBG did not cross the prespecified monitoring boundaries or reach the required information sizes. The certainty of evidence for all outcomes was rated as low or very low.

CONCLUSION: Probiotic/synbiotic supplementation may be associated with increased HDL-C and reduced FBG levels in patients with CHD. However, given the negative TSA findings, low certainty of evidence, and lack of hard cardiovascular outcomes, changes in HDL-C and FBG cannot be regarded as direct evidence of cardiovascular benefit. Furthermore, generalizability is limited, as five of the six studies were conducted in Iran and only one in China, which may limit applicability to populations with different dietary patterns, microbiome profiles, ethnic backgrounds, or healthcare systems. The substantial heterogeneity in probiotic strains, formulations, doses, and treatment durations also limits generalization to probiotics or synbiotics as a whole.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251178187; identifier: CRD420251178187.},
}

@article {pmid42997464,
year = {2026},
author = {Liu, X and Yang, W and Wang, Y and Peng, S and Zhou, J and Qiu, Q},
title = {Nasopharyngeal microbiota as a diagnostic biomarker for chronic rhinosinusitis with nasal polyps.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1865473},
pmid = {42997464},
issn = {2235-2988},
mesh = {Humans ; *Rhinosinusitis/diagnosis/microbiology ; *Nasal Polyps/diagnosis/microbiology/complications ; *Microbiota ; *Biomarkers/analysis ; *Nasopharynx/microbiology ; Chronic Disease ; RNA, Ribosomal, 16S/genetics ; Male ; Female ; Bacteria/classification/genetics/isolation & purification ; Adult ; Middle Aged ; Recurrence ; DNA, Bacterial/genetics/chemistry ; *Sinusitis/diagnosis/microbiology ; Sequence Analysis, DNA ; },
abstract = {BACKGROUND: Chronic rhinosinusitis with nasal polyps (CRSwNP) is a common inflammatory disorder with high postoperative recurrence rates. The nasopharyngeal microbiome may play a role in disease pathogenesis, but its diagnostic and prognostic utility remains unclear. This study characterized the nasopharyngeal microbiota in CRSwNP patients and evaluated its potential as a biomarker.

METHODS: 32 nasopharyngeal swab samples from CRSwNP patients and 11 from controls were collected and subjected to 16S rRNA gene sequencing. Microbial diversity, species composition, and differential abundance were analyzed. A diagnostic model was constructed using LASSO regression, with feature selection performed entirely within a 10-fold cross-validation framework, and model stability was validated via 100 Bootstrap resampling iterations. For recurrence prediction, due to the limited number of events (n=10), only exploratory univariate screening was conducted, and the stability of candidate biomarkers was evaluated using Bootstrap validation with internal feature selection (300 iterations).

RESULTS: CRSwNP patients exhibited significantly altered microbial composition at phylum and genus levels, as well as higher Shannon and Chao1 indices compared with controls, although the clinical and biological significance of this diversity increase requires further investigation. The three-genus combined diagnostic panel consisting of Fibrobacter, Ruminococcaceae_UCG-002, and Staphylococcus demonstrated favorable diagnostic performance. For recurrence prediction, Helicobacter and Parabacteroides were identified as stable candidate biomarkers, with Bootstrap selection frequencies of 24.0% and 27.3%, respectively. The recurrence-related findings are exploratory hypothesis-generating results and do not possess clinical predictive capability; they require validation in an independent large-cohort study.

CONCLUSIONS: The nasopharyngeal microbiota of CRSwNP patients exhibited significant alterations. The three-genus combined diagnostic panel demonstrated good discriminatory ability, supporting its potential as a non-invasive diagnostic biomarker. The identification of recurrence-related markers provides candidate targets for future research; however, due to the limited sample size, they currently lack clinical predictive capability. This study provides foundational data for microbiome research and clinical translation in CRSwNP.},
}

Humans
*Rhinosinusitis/diagnosis/microbiology
*Nasal Polyps/diagnosis/microbiology/complications
*Microbiota
*Biomarkers/analysis
*Nasopharynx/microbiology
Chronic Disease
RNA, Ribosomal, 16S/genetics
Male
Female
Bacteria/classification/genetics/isolation & purification
Adult
Middle Aged
Recurrence
DNA, Bacterial/genetics/chemistry
*Sinusitis/diagnosis/microbiology
Sequence Analysis, DNA

@article {pmid42997684,
year = {2026},
author = {Aggarwal, S and Grond, K and Miller, T and Kabir, F and Hasan, I and Matson, S and Dev, S and Drown, DM},
title = {Microbial and Water Quality Dynamics in a Utilidor-Housed Subsurface Drinking Water Distribution System Under Low-Use Conditions.},
journal = {ACS ES&T water},
volume = {},
number = {},
pages = {},
pmid = {42997684},
issn = {2690-0637},
abstract = {Cold-region utilidor-based drinking water distribution systems (DWDSs) are considered climate-resilient infrastructure but remain poorly characterized. Elevated temperatures and water age in such systems may accelerate disinfectant decay and microbial growth. We investigated water chemistry and microbiomes in a utilidor-housed subsurface DWDS serving a mixed-use sub-Arctic community during low demand following partial closure. Main and premise plumbing samples were collected over eight events spanning 14 months. Physicochemical measurements accompanied 16S rRNA gene amplicon sequencing. Temperatures increased from 7.2°C at the inlet to 31.9°C distally, while free chlorine residual declined significantly. Alpha diversity increased with distance and correlated negatively with disinfectant residual and dissolved oxygen. Microbial community composition differed significantly by location and time; Proteobacteria dominated most sites. Genera containing opportunistic pathogens included Legionella (80.7%), Mycobacterium (24.7%), and Pseudomonas (32.5%), with significant associations with total dissolved solids, nitrate, and dissolved organic carbon. These findings demonstrate that elevated temperatures and disinfectant decay may influence microbial communities and favor pathogen-associated taxa under low use. Utilidor-based DWDSs may, therefore, indicate vulnerabilities in buried systems under climate-driven warming and reduced demand. Results highlight the need for design and operational strategies addressing thermal control, water age, and disinfectant stability to protect drinking water quality in climate-stressed systems.},
}

@article {pmid42997884,
year = {2026},
author = {Siang, SC and Shan, CY and Fazhan, H and Waiho, K},
title = {Mud Crab Genus Scylla Broodstock Culture: Current Challenges and the Potential of a Hybrid Specific Pathogen Free Approach.},
journal = {Tropical life sciences research},
volume = {37},
number = {3},
pages = {1-14},
pmid = {42997884},
issn = {1985-3718},
abstract = {Mud crab (genus Scylla) farming forms an integral part of coastal aquaculture in Asia region, with their cultivation supporting coastal livelihoods, driving economic growth through their high market demand and promoting mangrove forest conservation and environmental sustainability via mangrove ecosystem integration. However, instability in the production chain, especially the early stages from broodstock cultivation to larval rearing and crablet, promoted the continued reliance on wild-caught broodstock. Such reliance on wild-caught broodstock introduces significant biosecurity risks, particularly through pathogen transmission and inconsistent reproductive performance. Current management selects mature females based on size and ovarian development, followed by acclimation and prophylactic formalin baths to mitigate bacterial and fungal infections. This review examines the biosecurity risks of relying on wild broodstock and proposes a practical "hybrid" approach that combines the innate immune resilience of wild populations with Specific Pathogen Free (SPF)-like conditions to enhance disease resistance, reproductive success and overall production sustainability. Nutritional strategies employ high-protein feeds, such as fish and bivalves, to enhance ovarian maturation, but untreated wild-caught feeds heighten pathogen transmission risks. By quarantine, disinfection and microbiome management protocol, pathogen load can be reduced while innate immunity can be improved.},
}

@article {pmid42992837,
year = {2026},
author = {El-Dougdoug, NK and Magistrado, D and Perry, KI and Short, SM},
title = {Microbiota modulation impacts life history traits and mating success in male Aedes aegypti mosquitoes.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0046526},
doi = {10.1128/msphere.00465-26},
pmid = {42992837},
issn = {2379-5042},
abstract = {UNLABELLED: Aedes aegypti mosquitoes transmit multiple arboviruses, but population suppression through the mass release of sterile or incompatible male mosquitoes can effectively reduce populations. These methods depend on the reliable mass-rearing of healthy, robust males that can successfully mate with wild females. The microbiota is a critical component of the larval diet, and its modulation can dramatically influence life history traits relevant to mass-rearing and male quality. Here, we used axenic (microbe-free), monoxenic (inoculated with Escherichia coli), and "laboratory community" mosquitoes (inoculated with an undefined microbiota derived from laboratory mosquitoes) to show that longevity was significantly enhanced in axenic and monoxenic males compared to laboratory community males. Moreover, monoxenic males more efficiently obtained mates in non-competitive mating scenarios compared to laboratory community males. However, microbiota treatment had no effect on mating success when males from different treatments competed for a mate. Our findings suggest that the microbiota is a key determinant of male mosquito life history, with direct implications for optimizing production of males for control programs.

IMPORTANCE: The microbes found in association with mosquitoes are crucial to mosquito development and have the capacity to influence multiple life history traits. In the current study, we comprehensively and functionally evaluate the role of the microbiota in mating success and other life history traits of male mosquitoes. Males are crucial to disease transmission, via their role in mating, and via their use in mosquito population control. By focusing on males, the understudied sex in mosquito research, we provide novel and foundational insight into how microbial communities influence male life history traits and mating success. Moreover, our findings establish a critical framework for understanding how the microbiota may affect male quality, production efficiency, and performance in vector control programs that involve mass production of adult male mosquitoes.},
}

@article {pmid42992852,
year = {2026},
author = {Morabbi, SM and Bhowmik, N and Sutherland, S and Wylie, EA and Decker, RS and Al Daerwish, A and Pérez Pérez, M and Pascual, E and Lutter, EI and Philmus, B and Stubbendieck, RM},
title = {Differential metabolite production underlies disruption of the cystic fibrosis airway microbiota by pathogens.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0115726},
doi = {10.1128/msystems.01157-26},
pmid = {42992852},
issn = {2379-5077},
abstract = {Cystic fibrosis (CF) results in accumulation of mucus in the airways that promotes pathogen colonization, leading to respiratory exacerbations, lung failure, and death. The CF airway harbors a complex microbiota, including pathogens and oropharyngeal bacteria. Here, we reanalyzed 5,260 16S rRNA gene microbiota data sets to infer associations between members of the CF microbiota. We determined that pathogens are more likely to proliferate and dominate when present, while oropharyngeal bacteria are generally present at lower abundances. We found that higher diversity and increasing numbers of pairwise associations between bacteria were positively correlated with lung function. In contrast, dominance of the microbiota by pathogens was associated with loss of lung function. We determined that pathogens are largely negatively associated with each other and oropharyngeal bacteria, suggesting they are antagonistic toward other bacteria. As a first test of this hypothesis, we cultured 1,597 isolates from 96 people with CF and performed 12,542 coculture assays against eight representative pathogens and oropharyngeal bacteria, finding 23% of interactions resulted in inhibition. Among our isolates, Pseudomonas were the most inhibitory, but we observed variable activity between different isolates. We further found Pseudomonas aeruginosa isolates, even those from the same donor and time point, exhibited significant differences in their metabolome and bioactivity profiles that correlated with acquisition of mutations. Together, our results suggest that pathogens may disrupt the CF microbiota and proliferate in part through bioactive metabolite production. Furthermore, these data highlight that characterizing multiple isolates is necessary to capture the full landscape of chemically mediated interactions within microbiomes.IMPORTANCEThe cystic fibrosis (CF) airway harbors a complex microbiota, including oropharyngeal bacteria and opportunistic pathogens that establish chronic infections. We found that microbiota diversity is correlated with health and that a pathogen-dominated microbiota is associated with low lung function. We then inferred potential microbial interactions by determining abundance associations between CF genera, which suggested that pathogens antagonize other bacteria. To test this prediction, we cultured bacteria from people with CF and performed thousands of coculture assays, finding that approximately one-quarter of interactions resulted in growth inhibition. Pseudomonas broadly inhibited other members of the CF airway microbiota. However, we observed marked variability in bioactivity and metabolite profiles of Pseudomonas aeruginosa isolates, even from the same donor at the same time. Our results suggest that pathogens disrupt the CF microbiota, possibly through bioactive metabolite production, and that characterizing multiple isolates is necessary to capture the complete picture of interactions in these communities.},
}

@article {pmid42992936,
year = {2026},
author = {Hu, Y and Sun, L and Huang, Y and Jiang, F and Tong, X and Yang, J and Ju, Y and Yang, Z and Liufu, S and Hu, Y and Ma, W and Guo, R and Li, W and Zhang, T and Zhu, X and Zhang, Z},
title = {Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0113826},
doi = {10.1128/msystems.01138-26},
pmid = {42992936},
issn = {2379-5077},
abstract = {Short-read metagenomic sequencing has been widely applied in microbial research due to its high quality and decreasing cost. However, short reads are inherently fragmented, which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with significantly longer read lengths, helps overcome these limitations. Achieving complete and accurate genome recovery is the core goal of metagenomics. To address this challenge, we systematically evaluated and optimized the long-read metagenomic workflow, from sample processing to computational assembly, using the CycloneSEQ platform.IMPORTANCEOur results suggest that upstream experimental protocols are important contributors to long-read metagenomic performance within the evaluated framework. In particular, magnetic-plate DNA extraction, together with pretreatment, was associated with more favorable input and downstream sequencing-related characteristics for long-read analysis. These changes were also associated with broader microbial recovery in the evaluated data sets. Assembly benchmarking further showed that integrating matched long-read (CycloneSEQ) and short-read (DNBSEQ) data sets provided a favorable balance across multiple evaluation dimensions. In our fecal metagenomic data set, long-read-first assembly followed by short-read polishing showed strong overall performance when recovery, contiguity, and sequence accuracy were considered together, although workflow performance remained metric dependent.},
}

@article {pmid42992937,
year = {2026},
author = {Paulsen, AA and Roghair Stroud, MN and Halverson, LJ},
title = {Physiological, behavioral, and genetic factors that shape interactions in the plant growth-promoting maize rhizosphere synthetic community.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0088826},
doi = {10.1128/msystems.00888-26},
pmid = {42992937},
issn = {2379-5077},
abstract = {Profiling microbiomes is an important way to understand the function and composition of communities in the wild, but natural microbiomes are often highly complex and often unamenable to experimentation to reveal cause-and-effect relationships. By using a small group of cultivable strains to represent those found in the wild, synthetic communities are one solution to this problem. Here we describe the maize rhizosphere synthetic community (MARSc), a genome-enabled 31-member bacterial community representative of the diversity found on the roots of maize grown in Iowa soils. This community is built around Pseudomonas putida KT2440, a model maize rhizosphere colonist and synthetic biology chassis. We characterized microbe-microbe interactions and biofilm formation of MARSc members in a variety of environmental contexts, finding that both behaviors are broadly controlled by nutrient levels. Genomic analysis and microbiome profiling of these organisms revealed that annotated biofilm genes (such as surface attachment and exopolysaccharide production) were significantly correlated with rhizosphere abundance, but neither trait correlated to in vitro biofilm formation. In vitro interaction assay findings were surprisingly consistent with co-correlations of rhizosphere abundance among MARSc members on roots. Finally, we found that when applied to the roots, MARSc can increase maize biomass (dry weight) by up to 40%-50% under varying nitrogen fertilization levels. Altogether, MARSc is a useful tool for identifying some of the factors influencing rhizosphere microbiome assembly and will be a strong foundation for further work in this area.IMPORTANCEThe microbiome surrounding the roots of plants can play an integral role in plant health and growth, and it is composed of thousands of species of microbes that are specific to the plant and environment it is grown in. However, due to this complexity, little is known about the means by which microbiomes form. In this study, we developed the maize rhizosphere synthetic community (MARSc) to gain a better understanding of the formation and function of microbiomes on the roots of plants. This consortium consists of 30 bacterial isolates plus Pseudomonas putida KT2440, a model maize root colonist. In this study, we investigated the interactions between these organisms, their genomes, cultural characteristics, and growth on the roots of maize. We show that MARSc increases maize growth under low nitrogen fertilizer, suggesting it will be a useful tool for identifying the mechanisms behind microbiome formation and plant growth promotion.},
}

@article {pmid42992988,
year = {2026},
author = {Maalumi, O and Ben Moshe, Z and Blank, O and Barkan-Michaeli, R and Yona, AH and Sharabi, K},
title = {Microbiota-derived indole-3-propionic acid regulates glucose homeostasis via remodeling of hepatic mitochondrial metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2760041},
doi = {10.1080/19490976.2026.2760041},
pmid = {42992988},
issn = {1949-0984},
mesh = {Animals ; *Indoles/metabolism ; *Glucose/metabolism ; Homeostasis ; Mice ; *Liver/metabolism ; Hepatocytes/metabolism ; Gluconeogenesis ; *Gastrointestinal Microbiome ; Male ; Mice, Inbred C57BL ; *Propionates/metabolism ; *Mitochondria/metabolism ; *Mitochondria, Liver/metabolism ; },
abstract = {The gut microbiota produces metabolites that circulate to host tissues and are increasingly linked to metabolic health, yet the mechanisms by which individual microbial products regulate liver glucose metabolism remain poorly defined. Here, we identify the tryptophan-derived microbial metabolite indole-3-propionic acid (IPA) as a direct modulator of hepatic glucose production. In primary hepatocytes, a focused screen of indole metabolites revealed that several indole-containing compounds suppress glucagon-stimulated glucose output, with IPA selected for further characterization. IPA selectively reduced glucose production from mitochondrial-dependent gluconeogenic substrates while largely preserving glycerol-supported glucose production, suggesting that it does not simply shut down gluconeogenesis but instead alters how hepatocytes use metabolic fuels. Mechanistic analyzes showed that IPA redirects lactate-derived carbon away from glucose production and reshapes mitochondrial metabolism, including redox balance, ATP availability, and urea cycle-linked metabolic activity. These effects occurred without detectable disruption of proximal insulin or glucagon signaling, supporting a model in which IPA acts primarily through intracellular metabolic remodeling. In mice, endogenous IPA levels varied with nutritional state, and short-term IPA administration improved fasting glycemia and glucose handling in Western diet-fed animals. Finally, microbiome-depleted mice colonized with IPA-producing Clostridium sporogenes displayed increased circulating IPA and improved glucose tolerance compared with mice colonized with an IPA-deficient mutant C. Sporogenes strain. Together, these findings identify IPA as a microbial metabolite that directly connects gut tryptophan metabolism to hepatic mitochondrial function and systemic glucose regulation, highlighting a mechanistic gut-liver pathway with potential therapeutic relevance to metabolic disease.},
}

Animals
*Indoles/metabolism
*Glucose/metabolism
Homeostasis
Mice
*Liver/metabolism
Hepatocytes/metabolism
Gluconeogenesis
*Gastrointestinal Microbiome
Male
Mice, Inbred C57BL
*Propionates/metabolism
*Mitochondria/metabolism
*Mitochondria, Liver/metabolism

@article {pmid42993179,
year = {2026},
author = {Scranton, C and Obergh, V and Goforth, M and Ravi, K and Jayakrishna, P and Khan, A and Boone, SA and Gerba, CP and Ijaz, MK and Xu, FY and Krupp, K and Madhivanan, P and Cooper, KK},
title = {Characterization of household microbiomes from three unique cities around the world.},
journal = {Microbial genomics},
volume = {12},
number = {11},
pages = {},
pmid = {42993179},
issn = {2057-5858},
mesh = {*Microbiota/genetics ; Humans ; Metagenomics/methods ; *Bacteria/classification/genetics/isolation & purification ; India ; United Arab Emirates ; Cities ; United States ; RNA, Ribosomal, 16S/genetics ; Shotgun Sequencing ; Family Characteristics ; Metagenome ; Housing ; },
abstract = {Characterizing the household bacterial microbiome allows for a stronger understanding of the various microbes to which a person is exposed every day in their home. Exploring household microbiomes in different countries around the world increases our understanding of the impact human behaviour might have on niche microbial communities in the house. The goal of this study was to use shotgun metagenomics to characterize the microbiome from ten locations around the house in ten different houses from three countries (Mysuru, India; Dubai, United Arab Emirates (UAE); and Tucson, USA). There was a significant difference in alpha diversity between the three countries (ANOVA, P<0.001), with homes in Mysuru, India, showing significantly higher bacterial diversity compared with those in Tucson, AZ, USA and Dubai, UAE. Beta diversity analysis of the homes found that bacterial communities differed significantly by geographic location [permutational multivariate analysis of variance (PERMANOVA), P=0.001] and, within cities, by household location (PERMANOVA, P=0.001), with geographic location explaining 5.3% and household location explaining 7.3% of variation. Household location was a strong driver of diversity within each of the three cities individually, accounting for 14-18% of microbiome variation. The highest levels of bacterial diversity across the three cities were found underneath the toilet rim and within bathroom and kitchen sinks. A core microbiome of classes Actinomycetota and Gammaproteobacteria was found in all homes in all three cities. Within each city, a core microbiome was identified at the species level within specific household locations. Many bacterial taxa found in the homes were a part of the human-associated phyla Actinomycetota (e.g. genera Brevibacterium, Mycolicibacterium and Rhodococcus), Pseudomonadota (e.g. genera Acinetobacter, Moraxella, Paracoccus and Pseudomonas) and Bacillota (genus Streptococcus), which is comparable to previous studies. The household microbiome is variable across different locations within the house and on a global scale. Factors such as human activity, cultural practices, climate and surface type and use may drive this diversity. Characterizing the household microbiome on a global scale allows for a better understanding of what drives microbial diversity, increasing our understanding of how microbial communities are shaped by the environment and how humans influence their dynamics, as well as any risks to human health that the built microbiome may potentially pose.},
}

*Microbiota/genetics
Humans
Metagenomics/methods
*Bacteria/classification/genetics/isolation & purification
India
United Arab Emirates
Cities
United States
RNA, Ribosomal, 16S/genetics
Shotgun Sequencing
Family Characteristics
Metagenome
Housing

@article {pmid42993299,
year = {2026},
author = {Kaunisto, KM and Smolander, N and Tamminen, M and Stoks, R and Kylänpää, S and Sääksjärvi, IE and Vesterinen, EJ},
title = {The Invisible Web: Linking Diet and Gut Microbiota Across Time and Space in Odonates.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42993299},
issn = {1432-184X},
mesh = {Animals ; *Gastrointestinal Microbiome ; *Diet ; *Bacteria/classification/genetics/isolation & purification ; *Odonata/microbiology/physiology ; Finland ; Feces/microbiology ; Seasons ; RNA, Ribosomal, 16S/genetics ; Electron Transport Complex IV/genetics ; DNA Barcoding, Taxonomic ; Feeding Behavior ; },
abstract = {The complex relationship between insects and their gut microbiota has become a central theme in host-microbe ecology, revealing profound effects on host fitness and interactions. Yet, how gut microbial communities-and their primary determinant, diet-vary across space and time in natural insect populations remains largely unexplored. Understanding these dynamics is essential for linking microbial variation with host biology. We investigated bacterial gut microbiota and dietary patterns in two odonate species, Sympetrum vulgatum and Lestes sponsa, across their flight season and three locations in southern Finland. Using faecal DNA metabarcoding of the cytochrome c oxidase subunit I (COI) gene for diet and 16 S rRNA gene for gut microbiota, we examined spatiotemporal changes and their associations. Season, location, and host species affected both dietary and bacterial diversity. The observed parallel responses of dietary composition and microbial communities highlight that the same ecological factors shaping insect feeding behaviour also influence their associated microbiota, illustrating the dynamic and context-dependent nature of insect-microbe interactions in the wild and emphasizing the need for broader ecological perspectives in microbiome research.},
}

Animals
*Gastrointestinal Microbiome
*Diet
*Bacteria/classification/genetics/isolation & purification
*Odonata/microbiology/physiology
Finland
Feces/microbiology
Seasons
RNA, Ribosomal, 16S/genetics
Electron Transport Complex IV/genetics
DNA Barcoding, Taxonomic
Feeding Behavior

@article {pmid42993389,
year = {2026},
author = {Toksanbaevich, ZK and Awulibieer, M and Maidanniyati, D and Hornok, S and Rysbayuli, SA and Serik, K and Kairat, O and Zhumagadyrovish, BN and Mukhitdinovich, DV and Wang, Y and Hazihan, W},
title = {Identification of bacterial communities and tick-borne pathogens in the fowl ticks (Argas persicus) from Almaty Oblast, Turkistan Oblast, and Shymkent City of Kazakhstan.},
journal = {Experimental & applied acarology},
volume = {97},
number = {4},
pages = {},
pmid = {42993389},
issn = {1572-9702},
support = {AP23489750//the Scientific and Technical Projects for Sustainable Development of the Agro-Industrial Complex of the Republic of Kazakhstan 2024-2026,/ ; (82260399 and 81960379)//the National Natural Science Foundation of China/ ; 2025AA018//the Key Scientific & Technological Project of XPCC/ ; 2023TSYCTD0020//the Science & Technology Innovation Team Project of Tianshan Elite/ ; 2026001ZYWGHZSYJSTGXM65004985//Health Science and Technology Program of Xinjiang Uygur Autonomous Region/ ; },
mesh = {Animals ; Kazakhstan ; *Microbiota ; *Argas/microbiology/growth & development ; RNA, Ribosomal, 16S/analysis ; *Bacteria/isolation & purification/classification ; Coxiella/isolation & purification ; Chickens ; RNA, Bacterial/analysis ; Poultry Diseases/parasitology/microbiology ; },
abstract = {Argas persicus (the fowl tick) is native to Central Asia. In this study, a total of 671 soft ticks were collected from chickens in three sampling sites (Bakanas District, Almaty Oblast; Sayram District, Turkistan Oblast; Shymkent City), Kazakhstan. A total of 16 tick pools (10 ticks per pool) were used for 16 S rRNA gene-based microbiome profiling by sequencing the V3-V4 region. Subsequently, seven genetic markers were amplified for molecular detection of Anaplasma, Rickettsia and Coxiella. Alpha and beta diversity analyses revealed that A. persicus ticks in Bakanas District had the highest microbial richness and diversity, while the ticks in Shymkent City and Sayram District exhibited highly similar microbial community compositions. The microbiome was predominated by Proteobacteria, specifically the genera Rickettsia and Coxiella, especially in Sayram District and Shymkent City, and the relative abundance of the top 30 bacterial components differed among sampling sites. Three pathogens including unclassified Anaplasma sp., Rickettsia hoogstraalii and Coxiella burnetii were detected for the first time in A. persicus ticks in Kazakhstan. The unclassified Anaplasma sp. was prevalent in ticks associated with domestic poultry and migratory birds, while Rickettsia hoogstraalii tended to parasitize seabird-related ticks with high prevalence. In addition, Coxiella burnetii infection prevalence was higher in pastoral areas than in urban areas, and birds act as secondary transmission vectors. These findings reveal that tick-borne pathogens harbored by avian soft ticks deserve close attention, especially in Central Asia.},
}

Animals
Kazakhstan
*Microbiota
*Argas/microbiology/growth & development
RNA, Ribosomal, 16S/analysis
*Bacteria/isolation & purification/classification
Coxiella/isolation & purification
Chickens
RNA, Bacterial/analysis
Poultry Diseases/parasitology/microbiology

@article {pmid42993715,
year = {2026},
author = {Mennen, MC and Zulu, MZ and Mabatha, KC and Baguma, R and Skelem, S and Mbundwini, NN and Aremu, OO and Adriaanse, M and van Dijk, D and Pillay, P and Africa, S and Jones, E and Setshedi, M and Brink, A and Burgers, WA and Ntusi, NAB},
title = {Protocol for investigating the association between Helicobacter pylori exposure, antigen-specific serological responses, and resistant versus non-resistant hypertension in a South African cohort.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362215},
pmid = {42993715},
issn = {1932-6203},
mesh = {Humans ; *Helicobacter pylori/immunology ; South Africa/epidemiology ; *Hypertension/microbiology/immunology/blood ; *Helicobacter Infections/complications/immunology/microbiology ; Cross-Sectional Studies ; *Antigens, Bacterial/immunology ; Adult ; Female ; Male ; Middle Aged ; Bacterial Proteins/immunology ; },
abstract = {BACKGROUND: Hypertension is a leading contributor to cardiovascular morbidity and mortality, with poor control in low- and middle-income countries. Helicobacter pylori (H. pylori) has been associated with hypertension through inflammatory, endothelial, metabolic and immune pathways, but data from sub-Saharan Africa, particularly in resistant hypertension, are limited.

METHODS: This cross-sectional observational study will enrol 200 adults aged ≥18 at a tertiary academic hospital in Cape Town, South Africa: 80 with resistant hypertension, 80 with non-resistant hypertension and 40 with normotension. Participants will undergo standardised clinical assessment, blood pressure measurement, and collection of blood, urine and saliva. H. pylori exposure will be assessed using the Pylori DuoTect® point-of-care assay, which detects antibodies to CagA and FliD. Laboratory analyses will include lipid profile, inflammatory and nitric oxide-related markers, homocysteine, insulin indices, complete blood count, ghrelin, multiplex cytokine profiling and flow cytometric immunophenotyping. PAXgene® blood RNA samples will be retained for future exploratory analyses. Saliva will undergo exploratory H. pylori antigen testing using CerTest® kits, which are validated for stool rather than saliva. Saliva analysis will be exploratory, and results will not define the primary H. pylori exposure variable. Remaining saliva will be kept for potential future oral microbiome analyses not defined in this protocol. Multivariable logistic regression will evaluate associations between H. pylori exposure and hypertension phenotype, adjusting for demographic, lifestyle, and clinical covariates.

DISCUSSION: To our knowledge, this will be the first African study to integrate point-of-care H. pylori serology with detailed clinical, inflammatory, metabolic, and immunological profiling across resistant hypertension, non-resistant hypertension and normotension. Findings may clarify biological pathways linking H. pylori exposure to blood pressure dysregulation and inform future mechanistic and interventional studies.},
}

Humans
*Helicobacter pylori/immunology
South Africa/epidemiology
*Hypertension/microbiology/immunology/blood
*Helicobacter Infections/complications/immunology/microbiology
Cross-Sectional Studies
*Antigens, Bacterial/immunology
Adult
Female
Male
Middle Aged
Bacterial Proteins/immunology

@article {pmid42993867,
year = {2026},
author = {Chakraborty, T and Kashyap, SJ and Chetia, PD and Purkayastha, S},
title = {The carcinogenic transition: toxicological, metabolic, and microbiome consequences of Westernized high-heat culinary practices in Asian populations.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/10408398.2026.2756028},
pmid = {42993867},
issn = {1549-7852},
abstract = {Colorectal and prostate cancer incidence has risen rapidly in several industrializing Asian populations. Dietary-pattern explanations focus on macronutrients, but cooking method is rarely examined. We discuss a "carcinogenic transition" hypothesis, in which a shift from moist-heat cooking (≤100 °C) toward dry-heat techniques (≥150 °C) increases formation of heterocyclic amines (HCAs) and polycyclic aromatic hydrocarbons (PAHs) in food. We examine three components (the "Triple Threat" framework) that may be relevant to some populations: (1) dietary HCA/PAH exposure; (2) host variation in xenobiotic metabolism, including N-acetyltransferase 2 (NAT2), cytochrome P450 1A2 (CYP1A2), and aldehyde dehydrogenase 2 (ALDH2) variants, which may alter bioactivation or clearance; and (3) diet-associated gut microbiome activity, including β-glucuronidase (GUS)-mediated deconjugation of excreted metabolites, supported by in vitro data with unquantified human magnitude. The framework rests on epidemiological associations and experimental mechanisms, not established causation. Confounding by obesity, alcohol, screening, and acculturation cannot be excluded, and trials isolating cooking method are needed. We also discuss practical food-preparation strategies, including lower-temperature cooking and antioxidant-rich marinades. Support comes from food-chemistry experiments and small urinary biomarker studies; effects on cancer incidence remain untested.},
}

@article {pmid42993877,
year = {2026},
author = {Zhang, Y and Teh, CE and Slaney, CY and Darcy, PK and Chong, MMW},
title = {Regulatory T Cell Interventions to Boost Anti-tumor Immune Responses.},
journal = {Cancer research},
volume = {},
number = {},
pages = {},
doi = {10.1158/0008-5472.CAN-26-0789},
pmid = {42993877},
issn = {1538-7445},
abstract = {FOXP3-expressing regulatory T cells (Tregs) are a specialized subset of T lymphocytes that are crucial for maintaining immune homeostasis and preventing autoimmunity. However, their pervasive presence and potent immunosuppressive functions within the tumor microenvironment (TME) are a barrier to anti-tumor immunity, presenting a major challenge for cancer immunotherapy. In this review, we discuss strategies for the therapeutic modulation of Tregs. Current and emerging promising technological approaches include antibody-based approaches, small molecule inhibitors, engineered Tregs, microbiome modulation, and Treg survival manipulations. Additionally, existing and promising combinatorial therapies integrate Treg cell targeting with complementary treatment strategies. The goal of this review is to spotlight how Treg-targeted interventions can overcome immune escape and ultimately enhance immunotherapy efficacy to improve clinical outcomes in cancer patients.},
}

@article {pmid42993880,
year = {2026},
author = {Ding, X and Du, Q and Ji, C and Chen, G and Li, J and Hu, W},
title = {Bacterial signals and mechanisms linked to the microbiota in calcium oxalate urolithiasis: Evidence boundaries and translational implications.},
journal = {Science progress},
volume = {109},
number = {4},
pages = {368504261506690},
doi = {10.1177/00368504261506690},
pmid = {42993880},
issn = {2047-7163},
mesh = {Humans ; *Calcium Oxalate/metabolism/chemistry ; *Urolithiasis/microbiology/metabolism ; Animals ; Oxalobacter formigenes/metabolism ; *Microbiota ; *Bacteria/metabolism ; Gastrointestinal Microbiome ; Crystallization ; },
abstract = {Calcium oxalate (CaOx) urolithiasis is traditionally interpreted through urinary supersaturation and metabolic risk, but emerging evidence suggests that bacterial signals and microbiota-derived metabolites may also influence crystal behavior, tubular epithelial injury, and stone-related host responses. This narrative review examines evidence from stone, urine, gut, and experimental studies, with emphasis on mechanistic evidence, compartment-specific findings, and the limits of current evidence. Human studies have detected bacterial signatures and cultivable organisms in CaOx-associated samples, but reported taxa and functional patterns vary across stone material, bladder urine, renal pelvis urine, voided urine, and stool, precluding a reproducible microbial profile. Experimental studies indicate that intact bacteria and bacterial products can modulate CaOx crystallization, crystal growth, aggregation, crystal-cell adhesion, epithelial injury, inflammation, and regulated cell-death pathways. Studies of the gut microbiota further implicate Oxalobacter formigenes-associated oxalate handling and microbiota-derived metabolites. However, direct pure-CaOx human evidence remains limited, and many mechanistic claims rely on mixed-calcium or preclinical contexts. Current evidence supports biological plausibility but not human causality, a universal microbial signature, or validated microbiota-targeted therapy. Future studies should prioritize standardized sampling, well-characterized CaOx cohorts, longitudinal validation, and clinically relevant recurrence endpoints.},
}

Humans
*Calcium Oxalate/metabolism/chemistry
*Urolithiasis/microbiology/metabolism
Animals
Oxalobacter formigenes/metabolism
*Microbiota
*Bacteria/metabolism
Gastrointestinal Microbiome
Crystallization

@article {pmid42994040,
year = {2026},
author = {He, T and Alai, W and Yang, Y and Hou, K and Ji, M and Han, Y and Yi, X and Zhou, N and Zhang, H},
title = {Microbiome-mediated regulation of growth and steroidal saponin biosynthesis in Paris species: Roles of endophytes and arbuscular mycorrhizal fungi.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128810},
doi = {10.1016/j.micres.2026.128810},
pmid = {42994040},
issn = {1618-0623},
abstract = {Paris species (Paris spp., Liliaceae) are important medicinal plants whose therapeutic value is largely attributed to their bioactive steroidal saponins. However, their slow growth, prolonged cultivation cycles, depletion of wild resources, and susceptibility to continuous-cropping problems constrain sustainable production and the improvement of medicinal quality. Elucidating the biological and environmental factors governing steroidal saponin accumulation is therefore essential for optimizing Paris cultivation and enhancing medicinal quality. This review focuses on the roles of endophytes and arbuscular mycorrhizal fungi (AMF) in regulating the growth and medicinal quality of Paris species. First, the biosynthetic pathways and spatiotemporal accumulation patterns of major steroidal saponins in Paris species are summarized, together with the effects of environmental factors on their accumulation. The diversity, distribution, and identification of microorganisms associated with Paris species are then reviewed, followed by a synthesis of the mechanisms through which these microorganisms regulate plant growth and steroidal saponin biosynthesis. These mechanisms encompass modulation of photosynthetic performance and phytohormone signaling, enhancement of stress tolerance and mineral nutrient acquisition, remodeling of the rhizosphere environment, regulation of heavy metal accumulation, microbial induction of secondary metabolism, and modulation of key genes involved in steroidal saponin biosynthesis. Finally, the potential applications of beneficial microorganisms in the development of microbial inoculants and the alleviation of continuous-cropping problems are discussed.},
}

@article {pmid42994041,
year = {2026},
author = {Li, W and Zhu, Q and Wu, Y and Zhu, J and Zhu, X and Li, L and Lin, F and Su, Z},
title = {A new species in the Magnaporthiopsis genus from wild rice enhances rice yield and disease resistance by restructuring the microbiome.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128816},
doi = {10.1016/j.micres.2026.128816},
pmid = {42994041},
issn = {1618-0623},
abstract = {Wild rice serves as a rich reservoir of beneficial endophytic fungi. However, the diversity and functional potential of these endophytes remain largely unexplored, limiting their utilization in sustainable rice production. In this work, we isolated and identified a novel endophytic fungus, Magnaporthiopsis oryzae (coded MB-9-27), from wild rice, Oryza granulata, and demonstrated that it directly promotes rice growth (yield increased by 12.66%) and enhances resistance to rice blast (disease rate decreased by 45.51%) in the field. Furthermore, MB-9-27 inoculation reshaped the rice microbiome, simplifying microbial interaction networks while significantly enriching beneficial bacteria (Methylobacterium sp., Sphingomonas sp.) and fungi (Mortierella sp., Rhizophagus sp., Mollisia sp., and Coniothyrium sp.). Among 75 fungi isolated from MB-9-27-treated rice plants, five representative strains (F14: Mortierella sp., F25: Trichoderma sp., F27: Clonostachys sp., F29: Podospora sp., and F30: Pseudeurotium sp.) corresponded to taxa ranked among the top 150 dominant fungal members identified through microbiome analysis. Functional screening revealed that Mortierella sp. (coded F14) markedly promoted rice growth, increasing shoot and root development by 55.8% and 51.6%, respectively, and reducing rice blast severity by 18.2%, indicating its dual role in promoting growth and suppressing disease. Metabolomic profiling of the rice-F14 holobiont identified significant accumulation of several metabolites, including Indole-3-glycerol phosphate (IGP), Adenine, and S-lactoylglutathione (SLG), suggesting alterations in pathways related to tryptophan metabolism, cellular metabolism, and redox homeostasis. Targeted LC-MS analysis further confirmed the production of IGP by F14. Bioassays demonstrated that IGP significantly promoted rice growth, supporting a potential role of tryptophan-derived metabolites in the plant growth-promoting activity of F14. Collectively, our findings demonstrated that MB-9-27 functions not only as a growth-promoting and disease-suppressive endophyte but also as a driver of beneficial microbiota assembly. Our results highlighted the potential of wild rice-derived endophytic fungi and their associated microbiota as valuable resources for microbial-assisted sustainable rice production.},
}

@article {pmid42994147,
year = {2026},
author = {Furtado, MM and Margalho, LP and Amorim-Neto, DP and Lemos Junior, WJF and Duarte, VS and Garcia, MV and Santos, AFM and Rodrigues, DP and Copetti, MV and Sant'Ana, AS},
title = {Bacterial and fungal community dynamics in black pepper (Piper nigrum) across different processing plants using culture-based and amplicon sequencing approaches.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112149},
doi = {10.1016/j.ijfoodmicro.2026.112149},
pmid = {42994147},
issn = {1879-3460},
abstract = {Black pepper (Piper nigrum) is among the most commercially relevant spices worldwide, yet its microbial ecology throughout processing remains insufficiently understood, particularly in relation to food safety. Despite being a low-water-activity product, black pepper may harbor diverse bacterial and fungal communities, including spoilage microorganisms, mycotoxigenic fungi, and foodborne pathogens. In this study, we investigated the dynamics of bacterial and fungal communities along the black pepper processing chain in three distinct processing plants. A total of 154 samples were collected from processing plants A, B, and C in São Mateus, Espírito Santo, Brazil. Culture-dependent analyses included enumeration of aerobic mesophilic bacteria, Enterobacteriaceae, lactic acid bacteria, total fungi, and xerophilic fungi; fungal isolation and identification; and Salmonella detection and confirmation. Culture-independent profiling was performed by amplicon sequencing targeting the V3-V4 region of the 16S rRNA gene and the V9 region of the 18S rRNA gene. Microbial counts increased throughout processing, indicating that post-drying operations represent critical contamination points. Fungal isolation revealed genera of hygienic and toxicological relevance, including Aspergillus, Fusarium, Penicillium, and Cladosporium. Salmonella was detected in 14.3% of the samples, comprising nine serotypes, with the highest occurrence after drying. Amplicon sequencing identified 5 phyla and 85 genera in the fungal community, whereas for the bacterial community, 24 phyla and 475 genera were identified, with Ascomycota, Proteobacteria and Firmicutes predominating across samples. Alpha and beta diversity analyses demonstrated significant differences among processing plants and confirmed processing as a major driver of microbial community assembly. Collectively, these findings reveal processing-associated microbial shifts and underscore the urgent need for improved hygienic practices, targeted monitoring, and effective decontamination strategies for black pepper.},
}

@article {pmid42994148,
year = {2026},
author = {Myung, GE and Min, SC},
title = {L-arginine supplementation in plasma-activated water (PAW) enhances the efficacy of PAW treatment for microbial inactivation and storage stability of grape tomatoes.},
journal = {International journal of food microbiology},
volume = {464},
number = {},
pages = {112135},
doi = {10.1016/j.ijfoodmicro.2026.112135},
pmid = {42994148},
issn = {1879-3460},
abstract = {This study investigated the antimicrobial efficacy of L-arginine-supplemented plasma-activated water (Arg-PAW) against Escherichia coli O157:H7 and Listeria monocytogenes inoculated onto grape tomatoes, as well as its effects on indigenous microbial growth, microbial community composition, and nutritional attributes, including lycopene and ascorbic acid, during storage. PAW and Arg-PAW were generated by treating 1 L of distilled water or L-arginine (L-Arg) solution (1 mg/mL), respectively, for 60 min using surface dielectric barrier discharge (SDBD) atmospheric cold plasma, with electrodes positioned above the liquid surface. Individual grape tomatoes were immersed without agitation in 500 mL of DW, L-Arg, PAW, or Arg-PAW at 23.0 °C for 5 min. L-Arg supplementation increased the nitrite, nitrate, and hydrogen peroxide concentrations in PAW from 25.3, 419.5, and 1.4 μM to 59.2, 1091.9, and 46.2 μM, respectively, while reducing the ozone concentration from 208.8 to 60.0 μM. Arg-PAW exhibited a higher pH and oxidation-reduction potential but lower electrical conductivity than PAW, with values of 3.0, 610.5 mV, and 1066.2 μS/cm, respectively. Arg-PAW achieved 3.8- and 3.2-log CFU/g reductions in E. coli O157:H7 and L. monocytogenes, respectively, slightly exceeding PAW, and showed lower Ascomycota and Pseudomonas abundances and Shannon diversity on day 3. During 14 days at 4 °C, Arg-PAW maintained lower indigenous mesophilic bacterial populations without adversely affecting color or pH. Lycopene remained stable, firmness was highest with Arg-PAW, and ascorbic acid increased during storage (p < 0.05). These findings indicate that L-Arg supplementation modified the PAW reactive-species profile and modestly improved microbial control while maintaining tomato quality.},
}

@article {pmid42994308,
year = {2026},
author = {Shen, D and Lv, Y and Wu, W},
title = {Bidirectional association and mechanisms between periodontitis and inflammatory bowel disease: A systematic review.},
journal = {International immunopharmacology},
volume = {191},
number = {Pt 1},
pages = {117639},
doi = {10.1016/j.intimp.2026.117639},
pmid = {42994308},
issn = {1878-1705},
abstract = {Periodontitis and inflammatory bowel disease are bidirectionally associated, yet the molecular mechanisms linking the two mucosal sites have not been systematically integrated. This systematic review synthesized these bidirectional pathways and identified core immunological hubs, following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. Mechanistic studies formed the core evidence, supplemented by population-based epidemiological and Mendelian Randomization studies; evidence strength was graded using a prespecified scoring system with a sensitivity analysis. Thirty-nine studies were included. Most mechanistic evidence derived from dextran sulfate sodium-induced (ulcerative colitis-like) colitis models, whereas validation in Crohn's disease-relevant models was limited. In the forward direction (periodontitis to inflammatory bowel disease), mechanisms comprised microbial translocation, metabolic disturbance, immune cell gut homing, and intestinal barrier disruption. The reverse direction was supported exclusively by preclinical models and is presented as a hypothesis. T helper 17 and regulatory T cell imbalance and dysregulated macrophage polarization constituted two shared hubs, interconnected via interleukin-1 beta and interleukin-17 A crosstalk. Macrophage polarization was the only hub with evidence in both directions, whereas Th17/Treg imbalance was robust only in the forward direction; however, a quality-restricted sensitivity analysis downgraded macrophage polarization to insufficiently supported. Preclinical modulation of either hub concurrently improved colitis and periodontitis, but clinical efficacy remains unestablished. These findings support a bidirectional association with mechanistic plausibility, although definitive causality is unproven. An asymmetrical dual-hub model is proposed for oral-gut axis research, predominantly in ulcerative colitis-like models; extrapolation to Crohn's disease requires independent validation.},
}

@article {pmid42994432,
year = {2026},
author = {Kohli, A and Hron, BM and Ebbeling, CB and Reyes, MM and Quealy, M and Gurry, T and Nguyen, LTT and Alm, EJ and Ludwig, DS and Zhang, YJ},
title = {Effects of dietary carbohydrate-to-fat ratio on the gut microbiome following weight loss.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {103137},
doi = {10.1016/j.xcrm.2026.103137},
pmid = {42994432},
issn = {2666-3791},
abstract = {Reducing dietary carbohydrates can improve metabolic health, yet the precise influence of carbohydrate restriction on the gut microbiome remains uncertain. Here, we report an ancillary study to the Framingham State Food Study, or FS(2), a controlled, randomized feeding trial involving adults with overweight and obesity. After a calorie-restriction phase to induce weight loss, we randomized participants to diets varying in energy from carbohydrate and fat (low-carb: 20% carb, 60% fat; moderate-carb: 40% carb, 40% fat; high-carb: 60% carb, 20% fat) for weight-loss maintenance for 20 weeks. Weight loss results in significant microbiome shifts, mirroring known associations. We do not detect compositional changes in the microbiome when diets vary carbohydrate-to-fat ratio, while controlling for other potentially confounding dietary factors. Changes in Shuttleworthia abundance correlate positively with maintenance of total energy expenditure following weight loss, suggesting a link between the gut microbiome and energy metabolism.},
}

@article {pmid42994532,
year = {2026},
author = {Wang, H and Shu, Z and Xie, Y and Zhang, L and Li, Q and Hu, Y and Gui, MY and Wang, M and Gu, MR and Zhu, L and Zhao, Y and Zhang, Y},
title = {Cord-serum Organophosphate Flame Retardants and Childhood Allergic Rhinitis: Multi-omics Insights.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.10.022},
pmid = {42994532},
issn = {1097-6825},
abstract = {BACKGROUND: Prenatal exposure to organophosphate flame retardants (OPFRs) may influence childhood allergic rhinitis (AR), but the potential involvement of the early-life gut microbiome and metabolome remains unclear.

OBJECTIVE: To evaluate associations between cord-serum OPFR concentrations and childhood AR and explore correlated microbial and metabolic pathways underlying these associations.

METHODS: OPFR-AR associations were evaluated in 1,255 children from the Shanghai Maternal-Child Pairs Cohort (MCPC), including 457 AR cases and 798 controls. Microbiome, metabolome, and exploratory correlated parallel-mediator analyses were conducted in a nested propensity-score-matched sub-study of 400 case-control pairs. Multiplicity was controlled within prespecified analysis-specific testing families using the Benjamini-Hochberg false-discovery-rate (BH-FDR) procedure.

RESULTS: Higher cord-serum concentrations of Tris (2-butoxyethyl) phosphate (TBEP) (adjusted odds ratio, OR=1.84, 95% CI: 1.63-2.09), tris(2-chloro-1-(chloromethyl) ethyl) phosphate (TDCPP) (OR=1.33, 95% CI: 1.04-1.70), and tri-m-cresyl phosphate (TMCP) (OR=1.05, 95% CI: 1.03-1.08) were associated with greater odds of childhood AR after multiple-testing correction. OPFR exposure and AR were also associated with bacterial genera and fecal metabolic features involving acetate and several tryptophan-related metabolites. Among 20 selected genus-metabolite models, 11 joint indirect associations met the full prespecified prioritization criteria.

CONCLUSION: Selected cord-serum OPFR concentrations were associated with childhood AR. Exploratory multi-omics analyses identified correlated bacterial and metabolic features consistent with potential indirect involvement in the OPFR-AR association.},
}

@article {pmid42994691,
year = {2026},
author = {Moran-Ramos, S and Alvarado-Calderon, J and Cerqueda-Garcia, D and Lopez-Contreras, BE and Villamil-Ramirez, H and Leon-Mimila, P and Aguilar-Salinas, C and Garcia, OP and Canizales-Quinteros, S},
title = {Children at risk of vitamin A deficiency exhibit taxonomic dysbiosis and functional remodeling of the gut microbiome: a matched case-control study.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101933},
doi = {10.1016/j.tjnut.2026.101933},
pmid = {42994691},
issn = {1541-6100},
abstract = {BACKGROUND: Vitamin A deficiency is one of the most prevalent micronutrient deficiencies worldwide. This condition increases susceptibility to infections and due to its role in intestinal barrier integrity, it has been suggested that it could predispose to gut dysbiosis.

OBJECTIVE: The aim of the study was to identify whether the gut microbiome of school-aged children at risk of vitamin A deficiency is associated with a dysbiotic state.

METHODS: This 1:2 matched case-control study for children at risk of vitamin A deficiency included thirteen school-aged children (6-9 years old) at risk of VAD and 26 with adequate vitamin A levels (VAA) from the ORSMEC cohort. Habitual diet was determined with a FFQ, plasma retinol levels were determined through HPLC, and gut microbial characterization was performed through shotgun sequencing.

RESULTS: In the present study, children at risk of VAD showed significantly higher levels of serum CRP (P=0.026). Although taxonomic gut microbial characterization showed no differences in alpha or beta diversity among groups, children at risk of VAD showed an enrichment of some facultative anaerobes, proposed to be established pathogens mainly from Streptococcus and Enterococcus genera (PFDR<0.1). At a functional level vitamin A status explained 7.09% of the variation in gut microbial functionality, when evaluated with the Bray-Curtis dissimilarity metric (P=0.008). Specifically, pathways related to pathogenicity such as O-antigen biosynthesis, heme biosynthesis and ethanolamine utilization were significantly enriched in children at risk of VAD (PFDR<0.1). In contrast, abundance of pathways related to B vitamins metabolism such as folate transformations, the super pathway for Coenzyme A biosynthesis and its precursor phosphopantothenate (vitamin B5) were depleted (PFDR<0.1).

CONCLUSION: Overall, our study showed that in school-aged children, being at risk of vitamin A deficiency is associated with an enrichment of potential pathobionts and a shift in gut microbial functionality that could be related to greater pathogenicity.},
}

@article {pmid42994723,
year = {2026},
author = {Agrawal, A and Lee, S and Chediak, A and Azizi, J and Labib, ME and Kulkarni, K and Gavette, M and White, J and Basile, R and Elson, N and Scott Phillips, K},
title = {Three-hospital study of endoscope protein contamination and microbiome.},
journal = {American journal of infection control},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ajic.2026.11.001},
pmid = {42994723},
issn = {1527-3296},
abstract = {BACKGROUND: Over 15 million colonoscopies and 7 million upper-GI endoscopies are performed annually in the United States, requiring reprocessing after each use to reduce infection risk. Methods for endoscope quality control are limited and require rapid turnover and high sensitivity/specificity.

METHODS: Here we explore two novel approaches to measure protein soil on endoscopes: turbulent fluid flow (TFF) extraction and extractionless assay for quick check of endoscope reprocessing (QC-ER). Microbial strains in extracted samples are characterized with Next-gen sequencing and PCR.

RESULTS: Both methods are suitable for clinical use. For TFF, 68 samples across three hospitals had an average pre-cleaning protein mass of 541±342µg and post-cleaning mass of 59±57 µg. For QC-ER, 63 samples across three hospitals had an average pre-cleaning mass of 66±52µg and post-cleaning mass of 28±33µg. None of 60 samples tested positive for microbes after high-level disinfection.

DISCUSSION: In method validation, both high level disinfection exposure and clinical sample matrices interfered with protein quantification by the bicinchoninic acid (BCA) assay. TFF and QC-ER detected soil that remained after simple rinsing. Differences in clinical results for pre-cleaning were likely due to post-procedure protocols. All levels were below consensus thresholds.

PRINCIPAL CONCLUSIONS: The amount of protein on endoscopes in healthcare facilities was quantified by these methods and fell within the expected range, with variations by type and age of endoscope.},
}

@article {pmid42994767,
year = {2026},
author = {May, L and Bajaj, JS and Wolstenholme, JT},
title = {The Gut-Liver-Brain-Lung Axis in Alcohol Use Disorder: Mechanisms and Therapeutic Implications.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {107470},
doi = {10.1016/j.alcohol.2026.107470},
pmid = {42994767},
issn = {1873-6823},
abstract = {Alcohol use disorder (AUD) is a multi-organ disease associated with an increased risk of severe pneumonia and acute respiratory distress syndrome (ARDS). While alcohol-related lung disease has often been attributed to ethanol-mediated injury to the alveolar epithelium, new evidence suggests a more broad and integrated model in which pulmonary vulnerability arises as a consequence of dysregulation in the gut-liver-brain axis. This review proposes a framework to explain how chronic alcohol consumption induces dysregulation in the gut-liver-brain axis and subsequently primes the lung for failure when a secondary hit, such as sepsis or infection, occur. Drawing on human observations and mechanistic studies in experimental preclinical models, we outline four candidate pathways that may link alcohol-related gut, hepatic, and neuroimmune changes to pulmonary vulnerability: 1) alcohol induces gut barrier disruption and dysbiosis, leading to the escape of lipopolysaccharides (LPS) into circulation; 2) the liver transitions to an amplifier of inflammation, releasing inflammatory signals into systemic circulation; 3) simultaneously, neuroimmune circuits such as the vagal cholinergic anti-inflammatory pathway and the hypothalamic-pituitary-adrenal axis are disrupted by chronic alcohol exposure, resulting in delays in resolving inflammatory responses; and 4) the lungs receive these inputs on a background of glutathione depletion and innate immune dysfunction, resulting in an environment that may appear normal at baseline but is primed to fail. Recognizing alcohol-related lung disease as a potential consequence of altered gut-liver-brain signaling in the context of chronic alcohol use could provide a foundation for developing targeted therapeutic strategies for ARDS in individuals with AUD.},
}

@article {pmid42994768,
year = {2026},
author = {Blinchevsky, N and Weed, M and Liangpunsakul, S and Llorente, C and Melamed, E},
title = {Vagus Nerve Stimulation as a Potential Therapeutic Strategy for Alcohol Use Disorder.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {},
number = {},
pages = {107469},
doi = {10.1016/j.alcohol.2026.107469},
pmid = {42994768},
issn = {1873-6823},
abstract = {Alcohol use disorder (AUD) contributes to approximately 3 million deaths worldwide each year and leads to substantial emotional, financial, and social implications for individuals and their families. AUD leads to multi-system damage, including the immune system, gut microbiome, neuroendocrine pathways, and the brain. Current treatments for AUD, focused primarily on behavioral and pharmaceutical interventions, insufficiently address alcohol's extensive impact on multiple body systems. Vagus nerve stimulation (VNS) has shown therapeutic benefits across a spectrum of neurological conditions, including epilepsy, depression, and addictive disorders. More recently, VNS is being investigated as a potential promising adjunctive treatment for AUD, which may complement currently used treatments by targeting many of the body systems dysregulated in AUD. Preclinical and clinical models have evaluated different VNS paradigms, including invasive, noninvasive, and minimally invasive approaches targeting motor and cognitive rehabilitation, withdrawal symptoms, and relapse during abstinence. However, while VNS has many promising potential benefits for improving AUD outcomes, direct evidence that VNS reduces alcohol consumption, alcohol seeking, or craving in AUD remains limited, and there are several logistical and ethical considerations that researchers, clinicians, and policymakers should evaluate before VNS is considered standard of care. Additionally, optimization of VNS parameters, modality (implanted versus noninvasive or minimally invasive), and development of responder biomarkers could better inform patient selection for VNS. Although significant work remains before transitioning VNS into clinical practice, VNS offers an exciting opportunity for adjunctive treatment in AUD that could potentially target multi-system AUD dysfunction.},
}

@article {pmid42994801,
year = {2026},
author = {Salas-Salvadó, J and García-Gavilán, J and Ni, J and Hernández-Cacho, A and Plaza-Diaz, J},
title = {Perspective. Precision Nutrition at a Crossroads: From Biological Prediction to Contextual Implementation.},
journal = {Advances in nutrition (Bethesda, Md.)},
volume = {},
number = {},
pages = {100764},
doi = {10.1016/j.advnut.2026.100764},
pmid = {42994801},
issn = {2156-5376},
abstract = {Precision nutrition has substantially reshaped nutritional science by demonstrating that individuals can respond differently to identical dietary exposures. Advances in genomics, metabolomics, proteomics, microbiome research, wearable technologies, digital health, and artificial intelligence have improved our ability to characterize biological heterogeneity and predict individual responses to diet. However, demonstrating such variability does not necessarily result in nutritional strategies that provide clinically meaningful benefits beyond established evidence-based care. A critical distinction should therefore be made between precision nutrition as a discovery science, which has convincingly established interindividual heterogeneity in dietary responses, and precision nutrition as an intervention science, which must demonstrate meaningful incremental value over dietary approaches already supported by clinical evidence. Despite increasingly sophisticated technologies and predictive models, evidence of consistent improvements in long-term health outcomes, cost-effectiveness, scalability, and equity remains limited. In this Perspective, we argue that precision nutrition has reached a critical crossroads. We distinguish prediction of individual responses, which is only one route to precision nutrition, from treatment-effect heterogeneity, treatment selection and clinical utility. We then propose contextual precision nutrition as a translational framework that integrates biological responsiveness with the behavioral, psychological, social, cultural, economic, and environmental determinants of dietary behavior. Rather than claiming novelty for these components, the framework integrates them into a decision logic that asks whether biological information improves the selection of a dietary strategy beyond routine information and established care, and how that strategy can be delivered and sustained. It complements population-based dietary recommendations by refining their implementation and maximizing adherence and real-world effectiveness. Ultimately, the success of precision nutrition will be determined not by the sophistication of its predictions but by its ability to translate biological knowledge into interventions that are clinically effective, scalable, equitable, and sustainable, thereby improving both individual and population health.},
}

@article {pmid42994968,
year = {2026},
author = {Yuan, X and Wu, L and Wang, Y and Zhao, Y and Zhou, L and Zhao, J},
title = {From systemic to oral: Unifying immunological mechanisms via the gut microbiome axis.},
journal = {Virulence},
volume = {17},
number = {1},
pages = {2750615},
doi = {10.1080/21505594.2026.2750615},
pmid = {42994968},
issn = {2150-5608},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; Animals ; Intestinal Barrier Function ; Dysbiosis/immunology/microbiology ; *Mouth Diseases/immunology/microbiology ; Fecal Microbiota Transplantation ; Probiotics ; Immunity, Mucosal ; Mouth/immunology/microbiology ; },
abstract = {While the gut microbiome regulates host homeostasis and systemic disease via the gut-immune axis, its potential role in regulating oral diseases remains underexplored. This review examines how established gut microbiome-immune mechanisms may contribute to oral inflammation and their therapeutic potential. Gut microbiome dysbiosis may influence oral diseases through microbial metabolites, intestinal barrier dysfunction, inflammatory signaling, and immune regulation. Evidence from systemic diseases supports these mechanisms and provides a rationale for microbiome-targeted approaches, including probiotics, dietary interventions, and fecal microbiota transplantation. However, direct clinical evidence in oral diseases remains limited and heterogeneous. Future research should clarify bidirectional gut-oral interactions, standardize microbiome assessment and clinical outcomes. Well-designed clinical studies are needed to address these limitations and translate the gut-oral axis into meaningful interventions.},
}

Humans
*Gastrointestinal Microbiome/immunology
Animals
Intestinal Barrier Function
Dysbiosis/immunology/microbiology
*Mouth Diseases/immunology/microbiology
Fecal Microbiota Transplantation
Probiotics
Immunity, Mucosal
Mouth/immunology/microbiology

@article {pmid42995195,
year = {2026},
author = {Qi, W and Chen, X and Guo, H and Zhu, S and Zhou, Z and Xu, L and Yan, Q and Gu, FF and Liu, JX and Sun, HZ},
title = {Microbiome-derived proline dipeptides underpin improved nitrogen utilization efficiency in dairy cattle.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42995195},
issn = {2041-1723},
support = {no. 32322077//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
mesh = {Animals ; Cattle ; *Dipeptides/metabolism ; *Nitrogen/metabolism ; *Proline/metabolism ; Rumen/microbiology/metabolism ; Female ; Fermentation ; Milk/metabolism ; *Microbiota ; Dairying ; Metagenomics ; Metabolomics ; *Gastrointestinal Microbiome ; },
abstract = {Dairy production is constrained by low nitrogen utilization efficiency (NUE; milk N/intake N), leading to nitrogen losses and environmental pollution. Although the rumen microbiome is central to nitrogen turnover, the role of small peptides, a critical nitrogen pool, remains poorly understood. Here, we constructed a genome-resolved atlas of predicted small-peptide metabolism and integrated high-performance chemical isotope-labeling metabolomics with metagenomics in 30 dairy cows. Among 349 detected small peptides, proline-containing dipeptides were associated with higher NUE, together with an S15 peptidyl-peptidase with Xaa-Pro dipeptide-generating activity. In vitro rumen fermentation, metatranscriptomics and targeted quantification showed that proline-dipeptide accumulation coincided with transcriptional patterns consistent with nitrogen assimilation and amino acid biosynthesis. Bacterial incubation and heterologous expression confirmed that S15.001 hydrolyzed Xaa-Pro substrates. These findings identify a microbial proline-dipeptide axis associated with NUE and provide a basis for precision nutrition strategies targeting ruminal peptide metabolism.},
}

Animals
Cattle
*Dipeptides/metabolism
*Nitrogen/metabolism
*Proline/metabolism
Rumen/microbiology/metabolism
Female
Fermentation
Milk/metabolism
*Microbiota
Dairying
Metagenomics
Metabolomics
*Gastrointestinal Microbiome

@article {pmid42995217,
year = {2026},
author = {Brodeur, GM and MacFarland, SP and Brodeur, GC and Porter, CC and Villani, A and Malkin, D},
title = {Emerging strategies for paediatric cancer predisposition: detection, surveillance and prevention.},
journal = {Nature reviews. Clinical oncology},
volume = {},
number = {},
pages = {},
pmid = {42995217},
issn = {1759-4782},
abstract = {A substantial proportion of childhood cancers occur in children who are genetically predisposed to develop that cancer. Close surveillance of children with cancer predisposition syndromes enables early cancer detection and results in better survival outcomes and less therapy-related toxicity, although many more predisposition syndromes are likely to exist and remain undetected. Building on conventional clinical surveillance protocols, new approaches are being explored, including liquid biopsy, molecular or metabolic biomarkers, enhanced imaging and microbiome profiling for the purposes of both improved surveillance and the discovery of additional predisposing factors. Knowing the specific genes, expressed proteins and biological pathways associated with a specific cancer predisposition syndrome might permit the use of targeted agents or vaccines, as well as the introduction of lifestyle changes to delay, reduce or even eliminate the development of cancer. Preclinical studies investigating the risks and benefits of preventive interventions would be greatly aided by the identification or development of animal models that faithfully recapitulate human syndromes. The incorporation of artificial intelligence to complement the clinical and experimental assessment of cancer risk based on the syndrome, genotype, modifier genes, family history, environmental exposures and other factors will undoubtedly improve the management and, ultimately, the outcomes of children with an increased genetic risk of cancer. In this Perspective, we discuss strategies to identify new cancer predisposition genes, developing approaches to cancer surveillance, emerging efforts for cancer prevention in high-risk patients, and the role of artificial intelligence in improving data analysis and optimizing medical decision-making.},
}

@article {pmid42995255,
year = {2026},
author = {Winkler, MKH and Ash, SR and Barraclough, KA and Bluechel, C and Ferrell, N and Fissell, W and Freedman, BS and Gerritsen, KGF and Hassan, HA and Hentschel, DM and Hestekin, J and Hughes, A and Johnson, DG and Krendel, M and Li, Z and Locke, JE and Montserrat, N and Nishinakamura, R and Plisiewicz, A and Ratner, BD and Roberts, GV and Roy, S and Sirich, TL and Subramanya, AR and Wasse, H and Wiener, S and Wieringa, F and Wolf, K and Himmelfarb, J},
title = {An integrative roadmap for a new era of kidney replacement therapies.},
journal = {Nature reviews. Nephrology},
volume = {},
number = {},
pages = {},
pmid = {42995255},
issn = {1759-507X},
abstract = {Innovation in kidney replacement is entering a transformative era. Although precision medicine has driven major breakthroughs in disease-specific therapies, progress in translating next-generation kidney replacement strategies into practice has lagged. This updated Roadmap highlights a shift toward bold, integrative approaches that merge engineering, biology and patient-centred design. Emerging directions include reimagining filtration and tubular function through biomimetic membranes, cellular systems and organ-on-chip technologies, and simultaneously exploring microbiome modulation and sorbent-based strategies to reduce the uraemic toxin burden. Beyond improving survival, new solutions are being shaped by priorities of mobility, sustainability and quality of life, pointing toward wearable and implantable systems that move care beyond the clinic. Biologic frontiers such as xenotransplantation and stem cell regeneration are opening pathways to potentially curative therapies, although challenges in safety, equity and scalability remain. Central to these efforts is the need to embed patient perspectives and ensure that innovations align with lived experiences. This integrative approach calls for renewed investment, regulatory clarity and cross-sector collaboration to accelerate translation of advances into equitable therapies redefining the future of kidney health.},
}

@article {pmid42995260,
year = {2026},
author = {Morris, LM and Boucher, M and Service, C and Anderson, JT and Rainwater, TR and Parrott, BB and Goffredi, SK},
title = {Microbiome Diversity, Persistence, and Potential Symbiont Dynamics in Placobdella Leeches from American Alligators.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42995260},
issn = {1432-184X},
support = {2030763//National Science Foundation/ ; SC-1700590//United States Department of Agriculture's National Institute of Food and Agriculture/ ; DE-EM0004391//U.S. Department of Energy/ ; },
mesh = {Animals ; *Symbiosis ; *Leeches/microbiology/physiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Alligators and Crocodiles/parasitology ; *Bacteria/classification/genetics/isolation & purification ; Phylogeny ; },
abstract = {Placobdella leeches are common ectoparasites of reptiles that rely on microbial symbionts to supplement the nutritional limitations of blood feeding. Although the primary symbiont Reichenowia is documented, little is known about the broader microbial community or ecological factors that influence Placobdella microbiome assembly. Here, we characterized the whole-body microbiomes of seven Placobdella clades from American alligators (Alligator mississippiensis) across the southeastern United States. Sampling revealed four Placobdella lineages not previously reported from alligators, including several undescribed species. Placobdella microbiomes, based on 16S rRNA gene sequencing, were dominated by Actinobacteriota, Alphaproteobacteria, Bacteroidota, and Pseudomonadota (the former Betaproteobacteria). Although microbiome composition was not strongly structured by leech clade, geography, or habitat type, location-specific bacterial signatures were observed. Captivity experiments resulted in significant declines in microbial diversity, and persistence of four bacterial taxa. Comparisons between leech microbiomes and microbial communities on alligator skin revealed limited overlap. Additionally, while a distinct Reichenowia lineage was generally associated with each Placobdella species, multiple low-abundance Reichenowia variants were detected within individuals, and an identical Reichenowia variant occurred in sympatric Placobdella species. Together, these results identify a conserved candidate core microbiome in Placobdella and demonstrate that microbiome assembly in blood-feeding leeches reflects persistent symbiotic interactions and ongoing environmental acquisition.},
}

Animals
*Symbiosis
*Leeches/microbiology/physiology
RNA, Ribosomal, 16S/genetics
*Microbiota
*Alligators and Crocodiles/parasitology
*Bacteria/classification/genetics/isolation & purification
Phylogeny

@article {pmid42995425,
year = {2026},
author = {Fay, BP and Tam, J and Wrobel, JA and Huang, G and Chou, WE and Sheikh, SZ and Furey, TS and Sartor, RB and Guo, H and Ting, JP},
title = {The role of NLRC5 in human inflammatory bowel diseases and murine experimental colitis.},
journal = {Journal of immunology (Baltimore, Md. : 1950)},
volume = {215},
number = {11},
pages = {},
doi = {10.1093/jimmun/vkag263},
pmid = {42995425},
issn = {1550-6606},
support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; R01 DK138462//NIH/NIDDK/ ; R01 DK136262//NIH/NIDDK/ ; T32-CA009156//UNC-ITCMS/ ; //P40 OD010995/ ; //Crohn's and Colitis Foundation/ ; },
mesh = {Animals ; Humans ; *Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology ; Mice ; *Colitis/immunology/chemically induced/metabolism ; *Inflammatory Bowel Diseases/immunology/metabolism ; Disease Models, Animal ; Gastrointestinal Microbiome/immunology ; Mice, Knockout ; },
abstract = {Nucleotide-binding, leucine-rich repeat-containing (NLR) innate immune proteins have been implicated in inflammatory bowel diseases (IBD). NLRC5 is a key trans-activator of class I MHC (MHC-I) genes, but it is also found to regulate cytokines and cell death. Meta-analysis of 14 different human RNAseq or microarray data (total n = 1,093) revealed a consistent and strong association between IBD and heightened NLRC5 expression, suggesting a role for NLRC5 across diverse IBD patients. Furthermore, these data show a strong correlation of NLRC5 with inflammation and STAT1 signatures, suggesting that its role in human IBD may extend beyond its canonical role as a regulator of MHC-I, or that its expression is controlled by inflammation/STAT1. However, in the dextran sulfate sodium (DSS)-induced colitis mouse model, Nlrc5 protected against colitis, which mimicked B2m-/- mice lacking MHC-I. This Nlrc5-associated protection has been consistent across hundreds of mice over a decade in the hands of several investigators. Microbiome study found significant alterations in the microbiota in overall composition and strain-specific differences over time, suggesting a dynamic relationship between microbiome dysbiosis and Nlrc5. To resolve these issues, we studied germ-free (GF) wild-type and Nlrc5-/- mice. Surprisingly, GF mice showed that Nlrc5 exacerbated instead of protected against DSS-induced colitis. A major difference between GF and conventionally-raised mice is that DSS reduced Nlrc5/ 2m expression in GF mice, while it did the opposite in SPF mice. These data highlight the complex role of Nlrc5 and the microbiome in the pathogenesis of IBD, as well as the necessity of complementary mouse models.},
}

Animals
Humans
*Intracellular Signaling Peptides and Proteins/genetics/metabolism/immunology
Mice
*Colitis/immunology/chemically induced/metabolism
*Inflammatory Bowel Diseases/immunology/metabolism
Disease Models, Animal
Gastrointestinal Microbiome/immunology
Mice, Knockout

@article {pmid42995442,
year = {2026},
author = {Yin, C and He, Y and Wang, P and Xu, Z},
title = {Hypersensitivity Pneumonitis: Clinical Paradigm Evolution, Immune-Driven Mechanisms, and Fibrotic Progression.},
journal = {Journal of immunology research},
volume = {2026},
number = {1},
pages = {},
doi = {10.1155/jimr/1288887},
pmid = {42995442},
issn = {2314-7156},
support = {82570097//National Natural Science Foundation of China/ ; 7262089//Natural Science Foundation of Beijing Municipality/ ; ZC201906243//Integrated Research Funding for Accumulated Projects of Peking Union Medical College Hospital/ ; },
mesh = {Humans ; *Alveolitis, Extrinsic Allergic/diagnosis/immunology/etiology/therapy/pathology ; Disease Progression ; Animals ; Idiopathic Pulmonary Fibrosis/immunology ; Adaptive Immunity ; Gene-Environment Interaction ; },
abstract = {Hypersensitivity pneumonitis (HP) is a complex immune-mediated interstitial lung disease (ILD) triggered by inhaled antigens in genetically susceptible individuals. Recent diagnostic paradigms have shifted from exposure-centric empiricism to fibrosis-based stratification and, most recently, separation of etiology from morphology, with fibrotic HP (FHP) now recognized as a progressive fibrotic phenotype distinct from yet overlapping with idiopathic pulmonary fibrosis (IPF). Mechanistically, HP progression reflects a sequential cascade involving gene-environment interactions, dysregulated innate and adaptive immunity, and maladaptive repair. Early disease is characterized by Th1/Th17-driven granulomatous inflammation, whereas chronic FHP exhibits Th2/M2 polarization, tertiary lymphoid structures, B-cell dysregulation, cellular senescence, lung microbiome dysbiosis, and persistent fibroblast activation, ultimately leading to progressively less reversible remodeling. Despite shared terminal pathways with IPF (e.g., extracellular matrix (ECM) deposition, EndoMT, and SASP), FHP may be conceptualized as predominantly inflammation-driven or "top-down," whereas IPF is often viewed as predominantly epithelial injury-driven or "bottom-up"; however, these heuristic models are not mutually exclusive and do not establish a discrete mechanistic transition or a uniform therapeutic window. Antigen avoidance remains the cornerstone of management; immunomodulatory treatment may be considered in selected inflammation-predominant phenotypes, whereas antifibrotic treatment may be considered when FHP meets criteria for progressive pulmonary fibrosis. The role of combined therapy remains uncertain, and strategies targeting IL-17, IL-6, or JAK-STAT remain investigational in HP. Early diagnosis is hindered by occult antigens and nonspecific presentations. Future advances will depend on multiomics integration, novel antigen-detection tools, and biomarkers that may help characterize the proposed transition from predominantly antigen-responsive inflammation toward fibrosis-dominant remodeling. Resolving whether a clinically meaningful transition exists may support a more mechanism-informed approach to HP. Unlike previous reviews focusing on diagnostic criteria, this review integrates our interpretation of the morphology-etiology distinction emphasized by the 2025 ERS/ATS classification update with single-cell-resolved immune evidence and uses the "immunofibrotic switch" as an integrative hypothesis rather than an established biological transition.},
}

Humans
*Alveolitis, Extrinsic Allergic/diagnosis/immunology/etiology/therapy/pathology
Disease Progression
Animals
Idiopathic Pulmonary Fibrosis/immunology
Adaptive Immunity
Gene-Environment Interaction

@article {pmid42995531,
year = {2026},
author = {Jentzsch, J and Wirtz, S and Brunner, M and Ribback, S and Kneis, B and Weber, K and Denz, A and Grützmann, R and Schierwagen, R and Tyc, O and Trebicka, J and Kersting, S and Langheinrich, M},
title = {Longitudinal gut microbiome dynamics in rectal cancer: associations with neoadjuvant therapy and tumor regression.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42995531},
issn = {1471-2180},
mesh = {Humans ; *Rectal Neoplasms/microbiology/therapy ; *Neoadjuvant Therapy ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Female ; Male ; Prospective Studies ; Feces/microbiology ; *Bacteria/classification/genetics/isolation & purification ; Longitudinal Studies ; Middle Aged ; Aged ; Treatment Outcome ; },
abstract = {BACKGROUND: The gut microbiome has emerged as a key modulator of colorectal cancer biology, influencing tumor progression and therapeutic response. However, most existing studies analyze colorectal cancer as a single entity despite biological and therapeutic differences between colon and rectal cancer. Consequently, longitudinal data linking microbiome dynamics to treatment response, particularly in rectal cancer, remain limited.

METHODS: In this prospective cohort study, 31 patients with rectal cancer were included, of whom 17 received neoadjuvant therapy and 14 underwent primary surgery. A total of 110 stool and tissue samples were collected at defined time points before, during, and after treatment. Microbial composition and diversity were analyzed using 16S rRNA gene sequencing. Alpha and beta diversity metrics, differential abundance analyses, and longitudinal comparisons were performed to assess treatment-related microbiome alterations.

RESULTS: Distinct microbial communities were observed between stool and tissue samples, with stool samples enriched in Bacteroidetes and tissue samples dominated by Firmicutes, Actinobacteria, and Verrucomicrobia. Neoadjuvant therapy was associated with a marked reduction in microbial diversity with no recovery before surgery, and community composition shifted significantly over the treatment course (patient-constrained PERMANOVA, p = 0.0016), with Clostridium XIVa becoming the dominant genus before surgery. Longitudinal analyses further revealed exploratory differences between patients with complete and incomplete tumor regression. Between diagnosis and surgery, patients achieving complete tumor regression (Dworak TRG 4) showed an increase in the propionate-producing genus Phascolarctobacterium, the only genus significant after correction for multiple testing, together with an exploratory rise in the butyrate-producing genus Roseburia. Higher Bacteroides in patients with incomplete regression was a descriptive observation that was not statistically significant (p = 0.35, q = 0.71). No genus-level differences between response groups were detected at baseline after correction for multiple testing; however, the small sample size limits the ability to exclude baseline differences.

CONCLUSIONS: Rectal cancer treatment induces distinct and time-dependent alterations in the gut microbiome. Complete tumor regression was associated with an increase in short-chain fatty acid-producing taxa, led by the propionate producer Phascolarctobacterium, whereas higher Bacteroides in incomplete responders was a non-significant, exploratory observation. Given the growing role of organ-preserving strategies such as watch-and-wait, in which reliable identification of complete response is critical, these exploratory patterns warrant validation in larger cohorts.},
}

Humans
*Rectal Neoplasms/microbiology/therapy
*Neoadjuvant Therapy
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Female
Male
Prospective Studies
Feces/microbiology
*Bacteria/classification/genetics/isolation & purification
Longitudinal Studies
Middle Aged
Aged
Treatment Outcome

@article {pmid42995617,
year = {2026},
author = {Swift, JF and Trello, GE and Harris, ZN and Migicovsky, Z and Miller, AJ},
title = {Conserved rhizosphere microbiomes and metabolic functions across diverse grapevine rootstocks: implications for plant elemental composition.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42995617},
issn = {2524-6372},
support = {2305703//National Science Foundation/ ; 1546869//National Science Foundation/ ; CRC-2021-00314//Natural Sciences and Engineering Research Council/ ; },
abstract = {BACKGROUND: While grapevine rootstocks are essential to commercial viticulture, researchers still lack a complete understanding of how these root systems and their associated microbiomes influence the vine's mineral nutrition. Previous research has shown that rootstocks with similar pedigrees, reflecting the limited number of parental genotypes in the breeding pool, affect both the vine's elemental profile and microbiome composition. Here, we extend this work by surveying a broader diversity of rootstock genotypes representing distinct parentage groups across multiple scions and by assessing both functional and taxonomic correlations between the rhizosphere metagenome and vine elemental composition.

RESULTS: We used a rootstock diversity trial with ten rootstock genotypes grafted to one of two scions to simultaneously characterize the rhizosphere metagenome and elemental composition of both berries and roots. We found that elemental composition varied strongly among vine compartments, while scion and rootstock had comparatively minor effects. Berries of 'Cabernet Sauvignon' contained higher concentrations of boron, potassium, and phosphorus than those of 'Chardonnay'. Only three elements in root tissues differed among rootstock genotypes, and these differences were unrelated to genetic relatedness among rootstocks. Rhizosphere microbiome composition was also conserved across rootstocks, suggesting that diverse genotypes recruit a consistent microbial community with similar functional potential. By linking rhizosphere microbiome profiles with root elemental composition, we found that Streptomyces and Mesorhizobium were significantly associated with elemental patterns, showing negative correlations with a principal component heavily loaded for molybdenum, cadmium, potassium, and iron.

CONCLUSIONS: Our findings suggest that vine compartment is a dominant influence on elemental composition, while rootstock genotypes have comparatively modest effects. Despite the overall conservation of the rhizosphere microbiome, specific microbial taxa were associated to elemental variation, highlighting potential microbe-element correlations that may influence nutrient dynamics in the grapevine rhizosphere. These results provide a step towards disentangling how root-associated microbes contribute to vine mineral nutrition, or vice versa, across diverse rootstock genotypes.},
}

@article {pmid42995884,
year = {2026},
author = {Karstens, L and Lamp, B and Kudrick, J and Siddiqui, N},
title = {Advances in 16S Taxonomic Classification: Impacts on Species-Level Resolution of Female Bladder Microbiota.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.759675},
pmid = {42995884},
issn = {2692-8205},
abstract = {Bacteria are present in the human urinary bladder, even in the absence of infection. These bacteria comprise the urinary microbiome, or urobiome, and have the potential to promote bladder health or contribute to pathology. Despite its importance, studying the urobiome remains challenging given the high proportion of host to bacterial cells and low microbial biomass. The leading method for studying the urobiome has been 16S rRNA amplicon sequencing. This culture-independent approach provides a cost-effective method for identifying bacteria, but taxonomic classification accuracy depends on three key factors: 1) the variable region targeted; 2) the reference database; and 3) the classification algorithm. In 2021, Hoffman et al. demonstrated that species-level classification of bladder microbiota was possible and that the database used was the most important factor, followed by the variable region. Here, we provide an updated analysis evaluating classification schemes using updated taxonomic databases, most notably GreenGenes2, and expand the analysis to full length 16S gene sequencing. We show that updated taxonomic reference databases improve the ability to identify bladder microbiota at the species level and that long-read sequencing of the full length 16S rRNA gene further improves species identification. These innovations may allow for enhanced discoveries when studying bladder bacteria in the context of bladder disorders.},
}

@article {pmid42995906,
year = {2026},
author = {Leon, F and Shih, JB and Keller, LE and Palaniappan, S and Degaetano, L and Nine, GA and Lind, AL},
title = {A novel clonal and axenic isolation pipeline for the human gut protist Blastocystis reveals within-subtype strain coexistence.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.19.760120},
pmid = {42995906},
issn = {2692-8205},
abstract = {UNLABELLED: Blastocystis is the most prevalent protist in the human gut microbiome, but its study is impeded by limitations in existing cultivation methods that hinder routine axenic and clonal isolation. These barriers have left open the question of whether multiple strains of a protist species can coexist within a single host, as observed within the bacterial gut microbiota. To address this, we introduce egg-based monophasic (EBM) medium, a novel optically clear liquid medium that supports exponential growth of Blastocystis from low inoculum densities in standard tissue-culture plates and flasks, a capability not supported by existing media formulations tested here. Using EBM medium, we established a modular axenization and clonal isolation pipeline and recovered axenic and clonally isolated cultures representing Blastocystis subtypes 1-4 from human and non-human primate hosts. To investigate within-host strain diversity, we sequenced a subtype 1 culture before and after clonal isolation. The non-clonal culture yielded a 21 Mb assembly with gene copy distribution and allelic polymorphism patterns consistent with multiple strains, whereas its clonal derivative yielded a 15 Mb assembly with patterns consistent with a single strain. These results indicate that the original culture contained multiple closely related strains co-colonizing one host. We identified the same genomic signature in published xenic cultures established from single human donors, supporting the presence of strain-level diversity within Blastocystis subtypes. Our pipeline provides a scalable platform for Blastocystis cultivation, imaging, and clonal isolation, enabling investigation of strain-level diversity that may be obscured in non-clonal cultures.

IMPORTANCE: Blastocystis is the most prevalent protist in the human gut, yet experimental investigation remains limited by a difficulty in obtaining single-microbe and genetically defined cultures. Existing methods make it difficult to separate the protist from associated bacteria or recover individual lineages from mixed cultures. We developed a liquid growth medium compatible with standard tissue culture plates, live-cell imaging, and a modular workflow for producing axenic and clonal isolates. We use this pipeline to create axenic and clonal isolates across four common subtypes. Applying this workflow exposed a mixture of closely related strains in a single-subtype culture, a finding supported by analyses of independent published cultures. This culturing pipeline enables controlled investigation of strain-level diversity, and provides a new experimental framework for the study of Blastocystis biology and its interactions with the gut microbiome.},
}

@article {pmid42995909,
year = {2026},
author = {Schiro, G and Patel, A and Tierney, E and Pasch, B and Upham, NS and Suzuki, TA},
title = {Conserved patterns of mammal-microbe codiversification and interspecific bacterial sharing.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.759742},
pmid = {42995909},
issn = {2692-8205},
abstract = {What determines whether a gut microbial lineage has fidelity to one host species or is shared freely across multiple species? Factors that predict microbial community composition, including host species, diet, and environmental variation, have been well documented in wild animals. However, the eco-evolutionary processes maintaining host species- or population-specific microbial lineages remain unresolved. Here, we analyze 519 gut microbiome samples collected from 15 species of wild rodents across two mountains in the Madrean Sky Islands of southeastern Arizona using full-length 16S rRNA sequencing. This montane system provides a natural experiment in which adjacent replicated elevational gradients bring different combinations of rodent species into sympatry, allowing host evolutionary history to be disentangled from shared environmental effects. We find that host phylogeny, rather than environment, is the primary driver of microbial strain sharing across host species. We recover replicated signatures of codiversification on both mountains, indicating shared evolutionary history between hosts and their microbes, despite ample opportunities for cross-species environmental transmission. This evolutionary coupling is associated with predicted differences in bacterial oxygen tolerance and optimal growth temperature: codiversifying lineages are predominantly obligate anaerobes with optimal growth near host body temperature, suggesting more limited out-of-host persistence than non-codiversifying taxa. This pattern mirrors findings from the human gut microbiome, suggesting conserved constraints on microbial dispersal across mammalian hosts. The cost-effectiveness of long-read amplicon sequencing for phylogenetic inference within bacterial species opens new opportunities for large-scale evolutionary and ecological studies of host-microbe interactions in wildlife.},
}

@article {pmid42995936,
year = {2026},
author = {Schedler, A and McCollough, K and Rogers, F and Macomb, K and Song, MJ and Ekwealor, JTB},
title = {Epiphytic cryptogam communities differ little despite strong variation in coastal fog exposure.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.16.759761},
pmid = {42995936},
issn = {2692-8205},
abstract = {Because mosses and lichens obtain water directly from their surroundings, coastal fog is expected to strongly influence epiphytic cryptogam communities during the long summer droughts of Mediterranean-climate ecosystems. We examined epiphytic mosses and lichens on coyote brush (Baccharis pilularis) across coastal and inland transects on San Bruno Mountain, California, where marine-layer exposure produces a sharp local microclimate gradient. We surveyed coyote brush availability, sampled standardized branches, monitored temperature and relative humidity, and quantified cryptogam occurrence, diversity, morphology, and reproduction. Morphological and chemical identifications were supplemented with molecular markers, while bacterial 16S sequencing was used to characterize cryptogam-associated microbiomes across host taxa and, for the dominant moss Pulvigera pringlei , across transects. Coastal microsites were cooler and more humid, whereas inland microsites experienced substantially greater daytime atmospheric drying demand. Despite this pronounced environmental contrast, cryptogam abundance, reproduction, and visible community composition differed little between transects, although branch-level genus diversity was modestly higher on the coastal transect. Macrolichen lobe or branch length and cryptogam patch area were greater inland in pooled comparisons, but these differences weakened after accounting for taxonomic composition. Bacterial communities differed strongly among cryptogam host taxa, but the P. pringlei microbiome showed no detectable difference in diversity or composition between coastal and inland transects. The broad similarity of cryptogam communities across a strong fog gradient is consistent with buffering of epiphytic cryptogams against fine-scale variation in marine-layer exposure. For the predominantly green-algal lichens in this community, the ability to absorb water vapor from humid air may reduce dependence on direct fog wetting, while host-associated bacterial communities may be structured more strongly by host identity than by local microclimate. Together, our results show that epiphytic cryptogam communities and microbiomes can remain remarkably similar across pronounced microclimatic variation despite modest morphological shifts.},
}

@article {pmid42995949,
year = {2026},
author = {Turabi, K and Sardarni, UK and Ankenbauer, KE and Torbit, SM and Taranto, CP and Dash, S and Meade, A and Cephas, AT and Klute, KA and Pasca di Magliano, M and McFall, T and DelGiorno, KE and Bailey-Lundberg, JM},
title = {Oncogenic KRAS-MAPK signaling sustains a CD73 dependent therapeutic vulnerability in pancreatic cancer.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.20.760559},
pmid = {42995949},
issn = {2692-8205},
abstract = {Pancreatic ductal adenocarcinoma (PDAC) is predominantly driven by oncogenic KRAS signaling and sustained by a desmoplastic, immunosuppressive microenvironment limiting therapeutic response. CD73-mediated adenosine signaling supports this immune-excluded, tumor-supportive microenvironment. Whether dual targeting of KRAS-MAPK and CD73 signaling creates a therapeutic opportunity to improve tumor control remains unexplored. Analysis of KRAS -mutant cancer cell lines revealed increased expression of NT5E and adenosine receptor ADORA2B . Pharmacologic and genetic suppression of oncogenic KRAS inhibited CD73 expression through a MAPK-dependent program. In syngeneic KPC tumors, conversely, CD73 inhibition with quemliclustat increased ERK phosphorylation in vivo , suggesting adaptive MAPK activation following CD73 blockade. Combined CD73 and RAS(ON) inhibition in vivo produced the strongest antitumor response, reducing endpoint tumor volume beyond either monotherapy. This combination significantly suppressed tumor proliferation and αSMA-positive stroma and resulted in a substantial reduction in CD163-positive macrophage infiltration. RAS-MAPK targeted therapy was also associated with increased CD8α-positive T cell infiltration and granzyme B-positive staining. As therapeutic responses in PDAC have been linked to the gut microbiome, we further examined treatment-associated changes in the microbiome. RAS-MAPK inhibition produced the most pronounced microbial alterations, which correlated with tumor volume and immune markers. Together, these findings identify KRAS-MAPK driven CD73 signaling as a therapeutic vulnerability in PDAC and support combined CD73 and RAS(ON) inhibition as a strategy to suppress tumor growth, remodel stroma, and alleviate tumor-associated immune suppression.},
}

@article {pmid42996130,
year = {2026},
author = {Vega-Rodríguez, J and Saraiva, FS and Silva, TAE and da Cunha, OT and Iniguez, E and Alvarenga, P and Barletta, A and Kudyba, H and Minai, M and Suzuki, M and Tolosano, E and Alves, D and Valenzuela, J and Barillas-Mury, C and Kamhawi, S},
title = {Mammalian Hemopexin Protects Blood-Feeding Dipterans from Heme Toxicity and Promotes Parasite Transmission.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10295862/v1},
pmid = {42996130},
issn = {2693-5015},
abstract = {Blood feeding exposes arthropod vectors and the pathogens they transmit to toxic heme released during hemoglobin digestion. Although mammalian blood proteins can cross the mosquito midgut into the hemolymph, whether they remain biologically active within the vector is unknown. Proteomic analysis of Anopheles gambiae hemolymph identified mammalian proteins enriched by Plasmodium infection, including several involved in heme and iron metabolism. This enrichment was dependent on parasite invasion of the midgut epithelium. We show that mammalian hemopexin, a high-affinity heme scavenger, retains its heme-binding activity within mosquito tissues, where it mitigates heme toxicity, preserves midgut barrier integrity and microbiome homeostasis, and promotes Plasmodium development. These protective effects were lost with recombinant hemopexin unable to bind heme, establishing heme scavenging as the underlying mechanism. Hemopexin also promoted Leishmania parasite development in the sand fly and supported the fitness of Aedes aegypti and sand flies. Thus, parasite induced-redistribution of host hemopexin establishes a functional link between mammalian heme homeostasis, vector physiology, microbiome homeostasis and pathogen development, revealing a previously unrecognized host-vector-pathogen interaction and a potential vulnerability for transmission-blocking interventions.},
}

@article {pmid42996160,
year = {2026},
author = {Yao, Y and Yang, Y and Song, J and Wu, L and Xu, M and Liu, H and Liou, YC and Xia, L},
title = {Intratumoral microbiota stratifies glioma malignancy and patient survival through metabolic associations.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1940097},
pmid = {42996160},
issn = {2235-2988},
mesh = {Humans ; *Glioma/microbiology/pathology/mortality/metabolism ; RNA, Ribosomal, 16S/genetics ; Female ; Prognosis ; *Microbiota/genetics ; Male ; Retrospective Studies ; Middle Aged ; *Brain Neoplasms/microbiology/pathology/mortality ; Tumor Microenvironment ; *Bacteria/classification/genetics/isolation & purification ; Survival Analysis ; },
abstract = {BACKGROUND: Glioma is the most common primary malignant tumor of the central nervous system, and its clinical outcomes remain highly heterogeneous despite advances in molecular classification and therapeutic strategies. Emerging evidence suggests that the intratumoral microbiome may influence tumor progression and the tumor microenvironment; however, its role in glioma malignancy stratification and prognosis remains poorly understood. This study aimed to characterize the intratumoral microbiota of glioma tissues and investigate its associations with tumor grade, overall survival, and potential metabolic regulatory mechanisms.

METHODS: A total of 107 treatment-naïve glioma patients were retrospectively enrolled, and tumor tissue samples were subjected to 16S rRNA gene sequencing to profile intratumoral microbial communities. Microbial sequence processing and taxonomic annotation were performed using QIIME2 and DADA2 pipelines. Microbial diversity and compositional differences were evaluated using alpha diversity analysis, Bray-Curtis distance-based principal coordinate analysis (PCoA), and differential abundance analysis. Kaplan-Meier survival analysis, univariate Cox regression, random forest feature selection, and multivariate prognostic modeling were performed to identify microbiome-associated survival indicators. Bootstrap optimism correction was performed with 1,000 resamples. PICRUSt2 was used to predict microbial functional profiles.

RESULTS: We found that intratumoral microbiota composition was significantly associated with WHO grade and overall survival. Positively associated taxa, including Firmicutes and Clostridia, were enriched in low-grade gliomas and favorable-prognosis groups, whereas negatively associated taxa such as Enterobacterales and Porphyromonas gingivalis predominated in high-grade gliomas and poor-survival patients. The model based on WHO grade-associated microbiota achieved optimism-corrected AUCs of 0.71, 0.86, and 0.88 at 1, 2, and 3 years, respectively. Functional prediction suggested differences in microbial pathways related to nucleotide biosynthesis and amino acid metabolism between groups.

CONCLUSIONS: Collectively, these findings suggest associations of intratumoral microbial signatures with glioma malignancy and prognosis, alongside differences in predicted microbial functional profiles. These exploratory observations warrant independent validation to clarify their biological and potential clinical relevance.},
}

Humans
*Glioma/microbiology/pathology/mortality/metabolism
RNA, Ribosomal, 16S/genetics
Female
Prognosis
*Microbiota/genetics
Male
Retrospective Studies
Middle Aged
*Brain Neoplasms/microbiology/pathology/mortality
Tumor Microenvironment
*Bacteria/classification/genetics/isolation & purification
Survival Analysis

@article {pmid42982526,
year = {2026},
author = {Mulligan, RJ and Cotobal Martin, C and Allerton, DM and Strickland, M and Bibby, I and Fachal, L and Watson, H and Bates, G and Beck, LC and Ahmad, T and Blackwell, J and Dart, RJ and Dong, C and Doona, M and Doyle, J and Fouweather, T and Gemmell, E and Hall, R and Irving, PM and Jacques, K and Kennedy, NA and King, AT and Lee, JC and Lees, CW and Lees, RD and Lindsay, JO and Masi, AC and Palmer-Jones, C and Parkes, GC and Parkes, M and Patel, KV and Povlsen, S and Powell, N and Prichard, J and Raine, T and Roberts, C and Samuel, E and Speight, RA and Subramanian, S and Reis, P and Vayreda, E and Wyatt, NJ and , and Stewart, CJ and Young, GR and McGregor, N and Anderson, CA and Lamb, CA},
title = {Open-IBD: protocol for a longitudinal multi-omics inception cohort in inflammatory bowel disease.},
journal = {BMJ open gastroenterology},
volume = {13},
number = {1},
pages = {},
pmid = {42982526},
issn = {2054-4774},
abstract = {INTRODUCTION: The clinical course of inflammatory bowel disease (IBD) is highly heterogeneous, yet the biological mechanisms underlying this variability, along with robust predictive biomarkers of disease course and treatment response, remain elusive. Most existing multi-omic cohorts recruit patients after IBD diagnosis and following therapeutic exposure, limiting the ability to distinguish between primary disease biology and downstream consequences of chronic inflammation and/or treatment. There is, therefore, a critical unmet need for large-scale, treatment-naïve inception cohorts integrating deep clinical phenotyping with longitudinal multi-omic profiling from the point of IBD diagnosis.

METHODS AND ANALYSIS: Open-IBD is a prospective, multicentre UK inception cohort study recruiting up to 2000 adults referred with suspected IBD, prior to diagnosis and initiation of IBD-specific therapy. Baseline assessment includes detailed clinical metadata collection, patient-reported outcome measures and collection of blood, stool and intestinal biopsy samples. 1000 participants subsequently diagnosed with IBD will be followed for up to 48 months, with repeated clinical assessments, questionnaires and biosampling. Participants not diagnosed with IBD will form a symptomatic control cohort with longitudinal clinical record review. Multi-omic analyses will include human genetics, single-cell transcriptomics of blood and intestinal tissue, stool and intestinal mucosal microbiome characterisation, metabolomics and proteomics. Integrated longitudinal clinical and multi-omic datasets will be generated to characterise early-stage treatment-naïve IBD, identify biomarkers associated with long-term outcomes and nominate causal factors driving IBD pathophysiology.

ETHICS AND DISSEMINATION: Ethical approval has been obtained from the Wales Research Ethics Committee 1 (24/WA/0338). All participants provide informed consent before enrolment. Recruitment is ongoing. Study findings will be disseminated through peer-reviewed publications, presentations at scientific meetings and lay summaries.

STUDY REGISTRATION NUMBER: ISRCTN15535639.},
}

@article {pmid42985524,
year = {2026},
author = {Bai, L and Zhang, Q and Zhu, J and Zhang, W and Cui, Z and Jia, T and Li, C and Guo, Z},
title = {Preventive effects of compound probiotics supplementation on migraine: Mendelian randomization analysis and experimental evidence.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1939532},
pmid = {42985524},
issn = {1664-302X},
abstract = {INTRODUCTION: Migraine imposes a substantial economic and societal burden. The microbiota-gut-brain axis (MGBA) has emerged as a key potential mechanism, yet its causal relationships with migraine and the underlying pathways remain unclear.

METHODS: We performed Mendelian randomization (MR) to assess the causal effects of gut microbiota on migraine, and further conducted mediation analysis to identify key mediating brain regions. In addition, we performed in vivo mouse experiments, in which we induced migraine-like pain via nitroglycerin (NTG) and investigated changes in gut microbiota, mechanical pain threshold, and regional brain activation following pretreatment with composite probiotics.

RESULTS: MR analysis identified eight gut microbial taxa causally associated with migraine and its subtypes. Mediation analysis suggested that the association between genetically predicted Paraprevotella abundance and migraine risk was partially mediated by ICVF in the posterior insular cortex. In NTG-induced migraine mice, composite probiotics ameliorated gut dysbiosis and maintained Paraprevotella abundance, while elevating mechanical pain thresholds in both periorbital and hind paw region. Probiotics intervention also suppressed c-Fos expression in the pIC, Sp5c, PVT, and mPFC. Additionally, it specifically decreased CGRP immunoreactivity in the Sp5c.

CONCLUSION: This study provides genetic and experimental evidence supporting a potential role of the gut microbiome in migraine and the potential of microbiome-based strategies for migraine prevention.},
}

@article {pmid42985593,
year = {2026},
author = {Hoza-Frederick, E and Martínez-Campos, S and Barber, PH and Vasquez, MI and Fotopoulos, V and Antoniou, C and Drakou, K and Godoy-Vitorino, F and Chiquillo, KL},
title = {Better together? Microbial communities associated with enhanced growth of the invasive seagrass Halophila stipulacea when mixed with a native Mediterranean seagrass Cymodocea nodosa.},
journal = {Frontiers in Marine Science},
volume = {13},
number = {},
pages = {1871379},
pmid = {42985593},
issn = {2296-7745},
support = {P20 GM103475/GM/NIGMS NIH HHS/United States ; },
abstract = {INTRODUCTION: Microorganisms are increasingly recognized as important contributors to the invasion success of introduced species into new environments. The globally invasive seagrass Halophila stipulacea flourishes in mixed species assemblages with native seagrasses, where it exhibits enhanced growth, while, in contrast, native seagrasses in mixed environments experience reduced growth. Here, we hypothesize that microbes may support the success of invasive seagrass in mixed Mediterranean environments.

METHODS: We analyzed 16S rRNA genes to characterize phyllosphere microbial diversity associated with the Mediterranean-native seagrass Cymodocea nodosa and the invasive H. stipulacea when grown alone or together, alongside biochemical, morphological, and sediment nutrient measurements.

RESULTS: Overall, C. nodosa in monoculture harbored a microbiome exhibiting higher ASV richness and a distinct community composition than H. stipulacea. Variation in bacterial diversity associated with hydrogen peroxide (H2O2) and internode length suggests that microbial communities of the native seagrass might be shaped by its stress-related physiological condition. Conversely, H. stipulacea's microbiome was most abundant in mixed environments, with bacteria significantly reduced in monoculture, and bacterial diversity loosely associated with growth, suggesting that bacterial diversity patterns associated with H. stipulacea vary across competition contexts and may be associated with differences in performance in mixed environments.

DISCUSSION/CONCLUSION: Our findings suggest that invasive H. stipulacea in the Mediterranean Sea is capable of harboring distinct bacterial assemblages that may be associated with growth patterns observed when co-occurring with the native seagrass C. nodosa. Future work should center on the mechanisms driving H. stipulacea bacterial communities and investigating whether H. stipulacea actively determines its own microbiome, or whether it passively acquires its microbiome by environmental variables.},
}

@article {pmid42985619,
year = {2027},
author = {Kreimeyer, H and Gonzalez, C and Fondevila, MF and , and Canbay, A and Stärkel, P and Gonzalez, DJ and Schnabl, B},
title = {DUF6383-domain containing protein from Parabacteroides distasonis predicts survival in patients with alcohol-associated hepatitis.},
journal = {Gut microbes reports},
volume = {4},
number = {1},
pages = {2728306},
pmid = {42985619},
issn = {2993-3935},
support = {R01 AA020703/AA/NIAAA NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R01 AA031710/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; U01 AA026939/AA/NIAAA NIH HHS/United States ; },
abstract = {Intestinal dysbiosis is a hallmark of alcohol-associated liver disease (ALD) characterized by a higher abundance of unfavorable species and a reduction of beneficial species. In this study, we aimed to analyze the bacterial proteome of stool samples from patients with alcohol-associated hepatitis (AH) (n = 80), alcohol use disorder (AUD; n = 20), and controls (n = 19) from an international multicenter cohort using quantitative tandem mass tag (TMT)-based metaproteomic profiling. We validated our results in an independent multicenter cohort of 72 patients with AH at the genomic level using qPCR. We detected 2,364 bacterial proteins and identified distinct metaproteomic signatures separating controls, patients with AUD, and AH. Patients with AUD and AH were characterized by depletion of Firmicutes-derived proteins and enrichment of proteins from Bacteroidetes, Proteobacteria, and Actinobacteria. Eighteen bacterial proteins increased with disease severity, many with multifunctional "moonlighting" roles, including enolase and hexokinase. DUF6383 domain-containing protein from Parabacteroides distasonis is correlated with histological injury, inflammatory cell infiltration, and is linked to neutrophil degranulation in the host. Patients with a high abundance of DUF6383 domain-containing protein had significantly lower 90-day survival, and this association was validated by qPCR at the genomic level in a second cohort. Our findings show that microbial proteins are associated with disease severity and progression, and that DUF6383 domain-containing protein from P. distasonis is a potential prognostic biomarker for AH.},
}

@article {pmid42985998,
year = {2026},
author = {Yang, T and Li, M and Wu, X},
title = {Mechanistic Insights Into How Acupuncture Modulates Host Immunity via the Gut Microbiota-Macrophage Axis.},
journal = {Immunity, inflammation and disease},
volume = {14},
number = {11},
pages = {},
pmid = {42985998},
issn = {2050-4527},
support = {//Jiangsu Road Sub-district Community Health Service Center, Shinan District, Qingdao/ ; },
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology ; *Macrophages/immunology ; *Acupuncture Therapy ; },
abstract = {BACKGROUND: Acupuncture is proposed to operate within the neuro-endocrine-immune network. Its therapeutic efficacy is proposed to be partly mediated through the gut microbiota-macrophage axis. This proposal is based primarily on preclinical findings. This axis may act as a biological transducer that helps sustain systemic homeostasis[1]. This review synthesizes current evidence on how acupuncture may orchestrate a top-down regulation of the intestinal microenvironment through somato-vagal circuits, particularly those involving PROKR2-expressing sensory fibers.

MATERIALS AND METHODS: This narrative review examined recent preclinical and clinical literature on acupuncture, gut microbiota, metabolites, and macrophage polarization. Studies were selected by relevance and expert judgment. Evidence was organized around the proposed gut microbiota-macrophage axis.

RESULTS: In preclinical rodent models and some human studies, acupuncture has been reported to suppress pathogens such as Proteobacteria. It may also promote symbionts like Akkermansia muciniphila and butyrate-producing taxa. Butyrate promotes anti-inflammatory M2 macrophage polarization via histone deacetylase (HDAC) inhibition and G-protein-coupled receptor signaling. In rodent models, acupuncture has been shown to strengthen barrier integrity. It may upregulate tight junction proteins. It may also prevent lipopolysaccharide (LPS) translocation and suppress M1-driven cascades. These effects extend distally via the gut-lung and gut-brain axes.

DISCUSSION: It is important to note that this proposed cascade is primarily derived from preclinical rodent models, and direct evidence in humans that confirms all steps from vagal activation to macrophage reprogramming remains incomplete. Ultimately, acupuncture may serve as a potential eco-immunological therapy that restores balance between the microbiome and innate immunity. This framework provides a preliminary conceptual basis for the eventual development of personalized, biomarker-driven protocols for chronic inflammatory diseases, although this hypothesis requires rigorous causal validation.},
}

Humans
Animals
*Gastrointestinal Microbiome/immunology
*Macrophages/immunology
*Acupuncture Therapy

@article {pmid42986106,
year = {2026},
author = {Izquierdo, VS and Sousa, LM and Brauner, C and Berwanger, J and Vendramini, JMB and Ashrafi, N and Mimi, RA and Graham, SF and Cappellozza, BI and Moriel, P},
title = {Fecal microbiome and plasma metabolome responses to Bacillus-based direct-fed microbial supplementation in cow-calf pairs from late gestation through weaning.},
journal = {Journal of animal science},
volume = {},
number = {},
pages = {},
doi = {10.1093/jas/skag353},
pmid = {42986106},
issn = {1525-3163},
abstract = {This study evaluated the effects of supplementation of a Bacillus-based direct-fed microbial (DFM) on the plasma metabolome and fecal microbiome of multiparous beef cow-calf pairs. On day 0 (94 ± 19 days prepartum), 296 Brangus crossbred beef cows were randomly assigned to treatments consisting of free-choice access to a trace mineral supplement alone (CON) or combined (BAC) with Bacillus subtilis 810 and B. licheniformis 809 (3 g/head/day; 6.6 × 109 CFU/head/day) from day 0 to 330 (weaning). Blood was collected from cows on days 0, 30, and 60, and from calves at birth, day 150, and day 330 for targeted metabolomics. Fecal samples were collected from cows on days 0, 60, 150, and 330, and from calves on days 150 and 330 for 16S rRNA gene sequencing. On day 30, BAC cows had greater (P ≤ 0.05) plasma concentrations of seven conjugated bile acids and two ceramides, but reduced (P ≤ 0.05) isoleucine, 3-indoleacetic acid, and indoxyl sulfate, with 12 pathways upregulated and 3 downregulated. On day 60, BAC cows had greater (P ≤ 0.05) total diacylglycerol and select diacylglycerol and triacylglycerol species, but reduced (P ≤ 0.05) eicosapentaenoic acid (EPA) and polyunsaturated phosphatidylcholines, with 11 pathways downregulated. Treatment effects were not detected (P ≥ 0.14) for fecal bacterial phyla, genera, or alpha diversity in cows, except for greater (P ≤ 0.04) Clostridium butyricum and C. alkalicellulosi relative abundances in BAC vs. CON cows at weaning. In calves, 103 metabolic pathways were impacted at birth (P ≤ 0.05), with the most upregulated being alanine, aspartate, and glutamate metabolism pathways; BAC calves also had greater (P ≤ 0.04) plasma alanine, aspartate, proline, and EPA concentrations at birth. At day 150, BAC calves exhibited greater total triacylglycerol concentrations (P = 0.01) across 48 individual species and upregulation of MIF-mediated immune regulation pathways. At weaning (day 330), BAC calves had greater (P ≤ 0.05) plasma anserine and select triacylglycerols, but reduced (P ≤ 0.05) ceramides and tended to have reduced (P ≤ 0.10) branched-chain amino acids, with 17 metabolic pathways downregulated. These findings indicate that gestation-to-weaning Bacillus-based DFM supplementation altered the plasma metabolome of beef cow-calf pairs, with limited effects on the fecal microbiome, and these changes coincided with the previously reported improvements in calf preweaning growth, post-weaning immune response, and carcass quality.},
}

@article {pmid42986108,
year = {2026},
author = {Xu, Y and Zhang, C and Wu, Y and Zhuo, J and Shen, X and Zhou, Y and Jin, J},
title = {Metagenomic insights into the avian gut microbiome: novel viruses, antimicrobial resistance, and beyond.},
journal = {mBio},
volume = {},
number = {},
pages = {e0234326},
doi = {10.1128/mbio.02343-26},
pmid = {42986108},
issn = {2150-7511},
abstract = {Birds play crucial roles in shaping ecosystems, and their gut microbiomes significantly influence host physiology and pathology. Understanding the composition, functions, and dynamics of avian gut microbiomes is therefore essential. Recent advances in metagenomic and metatranscriptomic sequencing have greatly increased our ability to characterize the avian gut microbiome. This review presents a systematic summary of the current knowledge regarding the composition of the avian gut microbiome as revealed through high-throughput sequencing technologies. It provides a statistical overview of the predominant bacterial and viral taxa present in the gut microbiomes of 195 bird species, revealing a persistent trend toward the discovery of novel viruses, and gives insight into the gene functions of these taxa. Interestingly, in terms of both antimicrobial resistance and multidrug resistance, wild birds harbor a greater diversity of resistance types than poultry. This review also presents a discussion of the relationships of avian life stages and the living conditions of birds with the gut microbiome and highlights practical applications of microbiome regulation in poultry production. Building on this foundation, future research priorities are outlined, such as the study of archaea, fungi, protists, and novel viruses, ways of improving methods to reduce costs and standardize protocols, and the development of more extensive metagenomic and metatranscriptomic data resources. Ultimately, these efforts could provide a holistic understanding of the avian gut microbiome.},
}

@article {pmid42986189,
year = {2026},
author = {Tytgat, B and Seppey, C and De Maeyer, L and Frossard, A and Velazquez, D and Karsten, U and Frey, B and Quesada, A and Vyverman, W and Svenning, MM and Verleyen, E},
title = {Differential effects of moisture on surface versus mineral soil microbial communities in the High-Arctic.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag126},
pmid = {42986189},
issn = {1574-6941},
abstract = {Microorganisms play key roles in nutrient/carbon cycling and greenhouse gas fluxes in High-Arctic soils. However, the influence of soil conditions on tundra microbiomes remains poorly understood. Using high-throughput sequencing, we studied bacterial, fungal and micro-eukaryotic communities in surface soil-biocrust matrices and the underlying mineral soil along two environmental gradients in Svalbard. Both layers harboured highly different communities. Gravimetric water content and pH were the most important factors in explaining the variation in surface communities. Cyanobacteriota were the dominant phototrophs in wetter tundra soils, while Chlorophyta dominated drier ones. In mineral soils, soil texture explained community structure for all three groups, together with carbon-content and carbon: nitrogen-ratio for micro-eukaryotes and bacteria. Chloroflexota and Spirotrichea dominated mineral soils with high clay content, Actinobacteriota positively correlated with sand content. The effects of soil texture and water content were also reflected in co-occurrence networks. Surface communities split into two network clusters linked to either drier or wetter tundra. The mineral soil network was much less coherent, and clustering was related to soil texture. Our findings revealed the important interplay between soil layer, toposequence and soil microbiome in the High-Arctic. As precipitation patterns shift, the impact of topography on tundra microbial communities is likely to intensify.},
}

@article {pmid42986545,
year = {2026},
author = {Chamekh, A and Fersi, C and Souguir, D and Chouari, R},
title = {Impact of treated wastewater irrigation on soil pollution-induced community tolerance and microbiome dynamics.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42986545},
issn = {1573-0972},
mesh = {*Soil Microbiology ; *Agricultural Irrigation ; *Bacteria/classification/genetics/isolation & purification/drug effects ; *Microbiota/drug effects/genetics ; RNA, Ribosomal, 16S/genetics ; Metals, Heavy/analysis ; *Soil Pollutants/analysis ; Soil/chemistry ; *Wastewater/chemistry/microbiology ; Agriculture ; },
abstract = {The reuse of treated wastewater (TWW) for agriculture is widespread in arid regions, but its comparative short- and long-term impacts on soil and microbiome remain poorly understood. This study aims to evaluate the short-term (4-5 years) and long-term (20-25 years) effects of TWW irrigation on soil physico-chemical properties, bacterial community structure, and emergence of contaminant tolerance in Cebala Borj Touil (Tunisia). Samples from irrigated and non-irrigated control soils (n = 4) were analyzed using physico-chemical characterization, 16S rRNA amplicon sequencing, and pollution-induced community tolerance (PICT) via [[3]H]leucine incorporation after exposure to Cu, Zn, Pb and tetracycline. Long-term irrigation led to a drop in pH with a significant increase in salinity, organic matter, and heavy metal concentrations (reaching, on average, 55, 120, and 63 mg/kg for Cu, Zn, and Pb), accompanied by a significant increase in PICT tolerance indices compared to control soils and in the short term. 16S sequencing revealed changes in alpha diversity (Chao1, ACE), with short-term irrigation showing the highest bacterial richness, while long-term exposure induced a profound community reshuffling with the dominant emergence of specific genera such as Defluviococcus, Pseudarthrobacter, Nocardioides and Gaiella. In conclusion, the prolonged irrigation by TWW selects a microbial community tolerant to chemical constraints and enriched in key taxa, which are promising bio-indicators for environmental monitoring of contaminated agricultural soils.},
}

*Soil Microbiology
*Agricultural Irrigation
*Bacteria/classification/genetics/isolation & purification/drug effects
*Microbiota/drug effects/genetics
RNA, Ribosomal, 16S/genetics
Metals, Heavy/analysis
*Soil Pollutants/analysis
Soil/chemistry
*Wastewater/chemistry/microbiology
Agriculture

@article {pmid42986679,
year = {2026},
author = {Maloney, S and Folliard, NT and Karakaya, G and Waters, SM},
title = {Importance of rumen ciliated protozoa and current research techniques for their analysis.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {11},
pages = {},
pmid = {42986679},
issn = {1465-2080},
mesh = {Animals ; *Rumen/parasitology/microbiology ; *Ciliophora/genetics/classification/isolation & purification/physiology ; Ruminants/parasitology ; Methane/metabolism ; Microbiota ; RNA, Ribosomal, 18S/genetics ; },
abstract = {Rumen protozoa are an integral component of the ruminant foregut microbiome, with a profound influence on feed digestion, microbial ecosystem dynamics and enteric methane emissions. Although they represent only a small proportion of species richness, protozoa contribute significantly to microbial biomass and functions in fibre degradation, volatile fatty acid production, microbial protein turnover, pH modulation and hydrogen-mediated methanogenesis. In addition to highlighting their importance to rumen function, this review summarizes classical and contemporary methodologies for enumerating, identifying and characterizing rumen protozoa. These methodologies include microscopy, fluorescent staining, flow cytometry and molecular approaches such as 18S rRNA, ITS and 28S rRNA amplicon sequencing. All major rRNA primers widely used over the last two decades are catalogued and their coverage is evaluated against current databases, highlighting the superior taxonomic resolution provided by ITS-based markers. The integration of single-cell sequencing and long-read platforms with multi-omics approaches (metagenomics, metatranscriptomics and metaproteomics) and advanced bioinformatic tools enables genome-resolved and functionally informed analyses of rumen protozoa. Methodological advances are integrated with functional insights to elucidate the contributions of protozoa to rumen ecology, feed efficiency and methane output. Key research gaps are also identified, including the need for improved microscopy techniques, automated image analysis, optimized cryopreservation protocols and robust culturing systems. This synthesis provides a comprehensive resource for researchers in microbial ecology, animal nutrition and environmental science, enabling precise protozoal profiling and informing strategies to enhance livestock productivity while mitigating environmental impacts.},
}

Animals
*Rumen/parasitology/microbiology
*Ciliophora/genetics/classification/isolation & purification/physiology
Ruminants/parasitology
Methane/metabolism
Microbiota
RNA, Ribosomal, 18S/genetics

@article {pmid42986703,
year = {2026},
author = {Guo, K and Golob, J and Berinstein, J and Sheehan, J and Chey, WD and Higgins, PDR and Young, V and Rao, K and Singh, P and Bishu, S and Lee, A},
title = {Mucosal transcriptomic and fecal microbiome signatures associated with persistent symptoms in quiescent Crohn's disease.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag244},
pmid = {42986703},
issn = {1536-4844},
support = {//IBD Plexus program of the Crohn's & Colitis Foundation/ ; //The Leona M. and Harry B. Helmsley Charitable Trust/ ; DK124567/NH/NIH HHS/United States ; DK139095/NH/NIH HHS/United States ; HS027431/NH/NIH HHS/United States ; T32-DK062708/NH/NIH HHS/United States ; R01-DK125687/NH/NIH HHS/United States ; R01-DK118154/NH/NIH HHS/United States ; AI182787/NH/NIH HHS/United States ; DK123403/NH/NIH HHS/United States ; },
abstract = {BACKGROUND: Persistent symptoms in quiescent Crohn's disease (qCD + S) lack clear mechanistic explanations. Building on prior evidence linking qCD + S to sulfidogenic microbial metabolism, this study characterizes the underlying site-specific mucosal transcriptional programs and host-microbe interactions associated with qCD + S.

METHODS: We integrated paired metagenomic and transcriptomic data from a cross-sectional cohort of patients with qCD. Host-microbe interactions in the ileum and rectosigmoid colon were analyzed using differential expression, penalized regression, and sparse canonical correlation analysis.

RESULTS: qCD + S was associated with transcriptional differences in separate analyses of ileal and rectosigmoid samples. The ileum showed reduced expression of genes related to immune surveillance, whereas the rectosigmoid colon exhibited reduced chemokine-related and increased ribosomal gene expression. Multi-omic integration identified associations between previously identified sulfidogenic microbes and mucosal genes related to mitochondrial metabolism, epithelial homeostasis, and neurosensory signaling. Exploratory sparse canonical correlation analysis identified multivariate patterns involving oral-associated taxa and mucosal genes related to B-cell receptor signaling and RNA-processing.

CONCLUSIONS: Persistent symptoms in qCD are mucosal transcriptional differences and fecal microbial features. These findings suggest a model in which altered immune regulation, microbial sulfur metabolism, and downstream epithelial and metabolic stress pathways contribute to symptom persistence despite quiescent inflammation, but this model requires mechanistic validation.},
}

@article {pmid42986715,
year = {2026},
author = {Kozłowska, P and Borowiecka, A and Strzemkowska, M and Jaworska, Z and Nowak-Arkusz, M and Skrypnik, D},
title = {How Plants Feed Our Microbes: Plant-Based Diets and Gut Microbiota Modulation-A Systematic Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag157},
pmid = {42986715},
issn = {1753-4887},
support = {//Department of Family Medicine/ ; JAK0000049//Poznan University of Medical Sciences/ ; },
abstract = {CONTEXT: Diet is a key factor shaping gut microbiota composition and function, with important implications for human health. The growing popularity of plant-based dietary patterns has increased interest in their effects on the gut microbiota.

OBJECTIVE: This systematic review examines specific changes in gut microbiota among individuals following a plant-based diet (PBD), as well as shifts occurring after transitioning from an omnivorous diet.

DATA SOURCES: PubMed and Google Scholar were searched for articles reporting original English-language human and animal studies investigating the effects of PBDs on gut microbiota composition or function. Studies published from 2015 onward were primarily considered, with most included articles published during 2020-2024.

DATA EXTRACTION: Four reviewers independently screened records according to eligibility criteria and extracted data on study characteristics, populations, dietary patterns, and outcomes related to gut microbiota composition and function.

DATA ANALYSIS: A total of 37 studies met the inclusion criteria. A PBD appeared to promote the growth of short-chain fatty acid-producing and probiotic bacteria, which help maintain intestinal integrity and support carbohydrate metabolism and may offer protection against certain diseases. A PBD was also reported to encourage the growth of beneficial taxa such as Roseburia spp., Akkermansia muciniphila, Clostridium symbiosum, and Faecalibacterium prausnitzii, which are considered indicators of a healthy microbiome. An increased Bacteroidetes/Firmicutes ratio, which was found to be a common occurrence in study participants following a PBD, correlated with a lower body mass index (BMI) and a more favorable metabolic profile, supporting healthy weight maintenance. In addition, PBDs were also associated with improvements in alpha- and beta-diversity compared with omnivorous diets.

CONCLUSIONS: This review indicates that PBDs appear to beneficially influence the gut microbiota and may have positive effects on human health. Nonetheless, not all studies agree on the extent or direction of microbiota changes associated with dietary patterns.

PROSPERO registration No. [CRD420251229407]; link: https://www.crd.york.ac.uk/PROSPERO/view/CRD420251229407.},
}

@article {pmid42986980,
year = {2026},
author = {},
title = {Erratum for the Report "Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors".},
journal = {Science (New York, N.Y.)},
volume = {394},
number = {6824},
pages = {eaen6718},
doi = {10.1126/science.aen6718},
pmid = {42986980},
issn = {1095-9203},
}

@article {pmid42987300,
year = {2026},
author = {H, B and Sahu, S and Balakrishnan, D and Ramadass, B},
title = {Effects of Lactobacillus crispatus-Containing Probiotics and Metformin on Insulin Resistance, Inflammation, and Gut Microbiome in Polycystic Ovary Syndrome: Protocol for an Open-Label Randomized Controlled Trial.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e102121},
pmid = {42987300},
issn = {1929-0748},
mesh = {Female ; *Metformin/therapeutic use/pharmacology ; *Polycystic Ovary Syndrome/drug therapy ; Humans ; *Insulin Resistance/physiology ; *Probiotics/therapeutic use/pharmacology/administration & dosage ; *Gastrointestinal Microbiome/drug effects ; *Inflammation/drug therapy ; *Lactobacillus crispatus ; India ; Adult ; },
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) affects 9% to 12% of reproductive-age women worldwide, with higher prevalence reported in India. Its pathophysiology involves insulin resistance, hyperandrogenism, and chronic low-grade inflammation, increasingly linked to gut dysbiosis and lipopolysaccharide-driven toll-like receptor 4 signaling. Elevated calprotectin and suppressed acylated ghrelin (AGH) reflect this inflammatory-metabolic disruption. While metformin remains standard therapy, it does not address underlying gut dysbiosis. Lactobacillus crispatus, with its antibacterial and immunomodulatory properties, is a promising but untested gut-targeted adjunct. This trial evaluates whether combining metformin with L. crispatus supplementation improves metabolic and inflammatory outcomes beyond either therapy alone.

OBJECTIVE: This study aims to compare probiotic, metformin, and combination therapy for reducing insulin resistance in PCOS over 12 weeks and assess their effects on gut barrier integrity, microbiome composition, hyperandrogenemia, glycemic control, and clinical outcomes.

METHODS: This open-label randomized, hospital-based trial at the All India Institute of Medical Sciences, Bhubaneswar, will assess the effects of probiotic and/or metformin therapy in women aged 18 to 40 years diagnosed with PCOS per Rotterdam criteria. A total of 135 participants will be randomized equally into 3 groups: probiotics only, metformin only, and combination therapy. The 3-month intervention includes metformin (1000 mg per day) and a specified L. crispatus-containing probiotic (2 capsules per day). The primary outcome is the change in Homeostatic Model Assessment for Insulin Resistance (HOMA-IR). Key secondary outcomes include changes in serum and fecal calprotectin, AGH, total testosterone, and fecal microbiome profile.

RESULTS: Participant recruitment began in January 2026. As of August 30, 2026, 26 of the planned 135 participants had been enrolled. Enrollment and data collection are projected to conclude by December 2026; statistical analysis will begin after database lock, with study completion anticipated by June 2027 and publication targeted for mid- to late 2027.

CONCLUSIONS: This trial will provide critical, mechanistic evidence on whether the targeted action of L. crispatus can work additively with metformin to heal the intestinal mucosal barrier, arrest systemic endotoxemia, and rescue disrupted gut-brain-endocrine signaling. By validating this novel metabolic-inflammatory regimen against localized (calprotectin) and systemic (AGH and HOMA-IR) end points, this study intends to establish a highly integrated, microbiome-targeted therapeutic strategy capable of optimizing long-term metabolic and reproductive health outcomes in women with PCOS.},
}

Female
*Metformin/therapeutic use/pharmacology
*Polycystic Ovary Syndrome/drug therapy
Humans
*Insulin Resistance/physiology
*Probiotics/therapeutic use/pharmacology/administration & dosage
*Gastrointestinal Microbiome/drug effects
*Inflammation/drug therapy
*Lactobacillus crispatus
India
Adult

@article {pmid42987457,
year = {2026},
author = {Nazario, C and Solari, L and Sciara, M and de la Vega Elena, CD},
title = {Exploring normality: Mapping the endometrial microbiome in healthy reproductive-aged women from Argentina.},
journal = {Revista Argentina de microbiologia},
volume = {59},
number = {1},
pages = {100763},
doi = {10.1016/j.ram.2026.100763},
pmid = {42987457},
issn = {0325-7541},
abstract = {The human microbiome varies according to individual and geographic characteristics. The endometrial microbiome plays a relevant role in reproductive physiology; however, data from healthy South American populations remain scarce. This prospective observational study aimed to characterize the endometrial microbiome in healthy reproductive-aged women from Rosario, Argentina and to establish a regional baseline for future research. A total of 100 healthy women aged 22-50 years from Rosario, Argentina, were included. Endometrial samples were obtained by aspiration biopsy during the follicular phase of the menstrual cycle or under hormonal contraception. Microbiome analysis was performed using 16S rRNA gene sequencing targeting the V4 region on the Illumina NextSeq 500/550 platform (2×150bp). Bioinformatic analysis was carried out in QIIME2. Of the 98 samples successfully amplified, 86 met quality criteria and were included in the final analysis. The endometrial microbiome was predominantly composed of Firmicutes, particularly members of the Lactobacillaceae family. The most abundant species were Lactobacillus iners and Lactobacillus helveticus/crispatus. No significant differences in alpha diversity were observed among age groups; however, a progressive increase in Gardnerella, Prevotella, and Megasphaera was detected with advancing age. This study provides the first regional characterization of the normal endometrial microbiome in healthy Argentine women and establishes a reference framework for future studies addressing endometrial dysbiosis and reproductive disorders.},
}

@article {pmid42987462,
year = {2026},
author = {Song, W and Wei, Y and Tang, L and Wong, FL and Lam, HM and Prasad, R and Zhang, S},
title = {Exploring the wild soybean derived cross-kingdom SynCom for mitigating continuous cropping obstacles: potential links to fungus-associated bacterial dispersal and root exudate reprogramming.},
journal = {Plant physiology and biochemistry : PPB},
volume = {240},
number = {},
pages = {111928},
doi = {10.1016/j.plaphy.2026.111928},
pmid = {42987462},
issn = {1873-2690},
abstract = {Continuous cropping obstacles severely constrain global soybean productivity, yet scalable biological solutions remain limited. While continuous monoculture typically causes yield decline in cultivated soybean, its wild relative persists in the same soils for decades without apparent decline, suggesting the presence of a protective native rhizosphere. By integrating long-term field surveys, metagenomic profiling, and stress-directed cultivation, we established a multi-tiered rational design framework to construct a functionally complementary, cross-kingdom synthetic community from wild soybean rhizospheres. Using a reductionist hydroponic model to isolate direct microbial effects from the complexities of the soil matrix, a simplified bacterial-fungal consortium successfully mitigated CCO-associated stresses. Specifically, SSC mitigated the growth inhibition caused by continuous cropping obstacles, enhanced disease resistance, and reduced the accumulation of phenolic autotoxins in the rhizosphere. Regarding the mechanism of action, compartmentalized experiments suggest that fungal hyphae can act as bacterial carriers, facilitating bacterial dispersal and increasing the accumulation of beneficial bacteria in the plant rhizosphere, thereby promoting rapid root colonization. SSC reprograms root exudates, significantly upregulating the biosynthesis of flavone and flavonol biosynthesis, which may act as chemotactic inducers to recruit beneficial microorganisms to soybean roots. Our research reveals that the wild soybean microbiome is an exploitable reservoir, providing a practical framework for translating the resilience of the native microbiome into sustainable agricultural solutions.},
}

@article {pmid42987531,
year = {2026},
author = {von Hellfeld, R and Gade, C and Williams, RS and Derous, D},
title = {Lessons learned from model species: Molecular markers for anthropogenic pollutant toxicity in cetaceans.},
journal = {Marine pollution bulletin},
volume = {234},
number = {Pt 1},
pages = {120546},
doi = {10.1016/j.marpolbul.2026.120546},
pmid = {42987531},
issn = {1879-3363},
abstract = {The planet is currently facing a triple crisis driven by climate change, biodiversity loss, and pollution. While the effects of environmental contaminants on reproduction, neurological function, and immune processes are well established in model species, far less is known about their impacts on marine sentinels such as cetaceans. Although contaminant burdens can be quantified, there is a lack of validated biomarkers that reliably capture molecular and cellular effects, limiting robust impact assessment and conservation strategies. Cetaceans exhibit unique physiological and metabolic adaptations, including specialised lipid dynamics and life-history traits, complicating direct extrapolation from model organisms. Here, we review current knowledge of biomarkers associated with three major contaminant classes: persistent organic pollutants (POPs), heavy metals, and microplastics. Candidate biomarkers such as cytochrome P4501A1, acetylcholinesterase, and metallothioneins are well characterised in experimental systems but show inconsistent responses in cetaceans, influenced by ecological, physiological, and methodological factors. Emerging evidence indicates that microplastics may drive gut inflammation, microbiome disruption, and systemic stress responses, although validated biomarkers remain scarce. Overall, we highlight the limitations of single-marker approaches and the need for integrative frameworks capturing complex, multi-stressor responses across biological scales. Future efforts should prioritise robust, early-warning biomarkers that account for species-specific physiology, trophic ecology, and cumulative exposure. Progress will require cross-disciplinary collaboration, integration of multi-omics tools, and improved standardisation of methods. Strengthening biomarker frameworks in cetaceans is essential for advancing marine conservation and understanding shared risks to ocean and human health.},
}