@article {pmid42071306,
year = {2026},
author = {Zhong, C and Chen, K and Lin, S and Huang, Y},
title = {Obesity-Related Cognitive Impairment: An Update Overview of Mechanisms and Treatments.},
journal = {Expert reviews in molecular medicine},
volume = {28},
number = {},
pages = {e19},
doi = {10.1017/erm.2026.10049},
pmid = {42071306},
issn = {1462-3994},
support = {NSFC 82200871//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *Obesity/complications/therapy/metabolism ; *Cognitive Dysfunction/etiology/therapy/metabolism ; Animals ; Gastrointestinal Microbiome ; Brain/metabolism ; Insulin Resistance ; },
abstract = {BACKGROUND: Lifestyle changes and unhealthy eating habits have led to a sharp rise in obesity rates worldwide. Obesity is closely associated with a range of complications, including cognitive impairment and dementia. Accumulating evidence indicates that obesity negatively affects cognitive function and may increase the risk of neurodegenerative diseases. Conversely, cognitive dysfunction may further contribute to the development and progression of obesity. With growing attention in this field, obesity-related cognitive impairment has emerged as an important research focus at the intersection of metabolic and neurological disorders.

METHODS: This article reviews the potential mechanisms underlying obesity-related cognitive impairment and summarizes emerging therapeutic strategies.

RESULTS: The development and progression of obesity-related cognitive impairment involve multiple mechanisms, including insulin resistance, systemic and central inflammation, immune dysregulation, microcirculatory alterations and changes in neurotransmitters and synaptic plasticity. Recent studies have focused on the adipose tissue-brain axis and the microbiota-gut-brain axis, in particular, the targeted effects of extracellular vesicles released from adipose tissue and microbiota on the brain.

CONCLUSIONS: This article systematically reviews the mechanisms underlying obesity-related cognitive impairment and presents novel therapeutic strategies.},
}

Humans
*Obesity/complications/therapy/metabolism
*Cognitive Dysfunction/etiology/therapy/metabolism
Animals
Gastrointestinal Microbiome
Brain/metabolism
Insulin Resistance

@article {pmid42091223,
year = {2026},
author = {Tagoe, J and Ojha, B and Horne, S and Prüß, B},
title = {Azospirillum brasilense and tomato exudate or cytidine increase phytopathogen resistance and modulate phyllosphere/rhizosphere.},
journal = {Canadian journal of microbiology},
volume = {72},
number = {},
pages = {1-14},
doi = {10.1139/cjm-2026-0032},
pmid = {42091223},
issn = {1480-3275},
mesh = {*Solanum lycopersicum/microbiology/chemistry/metabolism ; *Azospirillum brasilense/physiology/genetics ; *Rhizosphere ; *Plant Diseases/microbiology/prevention & control ; Plant Leaves/microbiology ; Plant Roots/microbiology ; Pseudomonas syringae/pathogenicity ; *Disease Resistance ; *Plant Exudates/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; },
abstract = {Tomatoes are an important crop worldwide and phytopathogens can cause devastating losses. This study describes a treatment, consisting of Azospirillum brasilense Sp7 and either tomato seedling exudate or the exudate compound cytidine. The combination of A. brasilense Sp7 with cytidine showed a remarkable reduction of 83.4% in disease severity of tomatoes challenged with Pseudomonas syringae pv. tomato DC3000. Replacing cytidine with exudate was less effective at 71%, but the reduction in disease severity was still larger than by A. brasilense Sp7 alone at 55%. This reduction in disease severity was not paralleled by a decrease in P. syringae in leaf homogenates. Cytidine caused a 6.7 fold increase in A. brasilense Sp7 16S rDNA in root homogenates. In phyllosphere and rhizosphere, treatments modulated the microbial composition. In the phyllosphere, specific associations between treatment groups and bacterial orders could be computed. In the rhizosphere, principal component analysis revealed that variation along PC1 was dominated by the presence or absence of A. brasilense. Intriguingly, the inoculant caused an increase in the abundance of other Azospirillales species.},
}

*Solanum lycopersicum/microbiology/chemistry/metabolism
*Azospirillum brasilense/physiology/genetics
*Rhizosphere
*Plant Diseases/microbiology/prevention & control
Plant Leaves/microbiology
Plant Roots/microbiology
Pseudomonas syringae/pathogenicity
*Disease Resistance
*Plant Exudates/pharmacology
RNA, Ribosomal, 16S/genetics
Soil Microbiology

@article {pmid42144148,
year = {2026},
author = {Ullah, H and Huang, S and Pei, Q and Gui, P and Shi, H and Hu, X},
title = {A review on the system-level bioactivity of polysaccharides along the structure-target-microbiome axis.},
journal = {International journal of biological macromolecules},
volume = {367},
number = {},
pages = {152569},
doi = {10.1016/j.ijbiomac.2026.152569},
pmid = {42144148},
issn = {1879-0003},
abstract = {Polysaccharides are structurally diverse biological macromolecules whose functional properties extend beyond simple structure-activity relationships. This review synthesizes current literature on bioactive polysaccharides from fungal, plant, algal, marine, and microbial sources, spanning foundational studies to recent advances up to 2026, with emphasis on structural glycobiology, host-microbe interactions, and translational glycoscience. We propose the Structure-Target-Microbiome (STM) axis as a mechanistic framework in which polysaccharide bioactivity arises from the integrated interplay of molecular architecture, host receptor engagement, and microbiome-mediated biotransformation. Unlike conventional structure-activity models that correlate individual structural features with single endpoints, the STM axis integrates structural determinants (monosaccharide composition, glycosidic linkages, branching, molecular weight, and chemical modifications), microbial carbohydrate-active enzymes, metabolite production, and host physiological responses into a systems-level perspective. Accumulating evidence indicates that major polysaccharide classes, including β-glucans, pectins, hemicelluloses, arabinogalactans, sulfated marine polysaccharides, and microbial exopolysaccharides, exert biological effects through both direct host signaling and microbiota-dependent metabolic conversion. However, the literature also reveals substantial inconsistency, with many polysaccharides showing weak, absent, or context-dependent activity influenced by structural heterogeneity, purity, dosage, microbial composition, and experimental variability. Limited fermentability and inter-individual microbiome differences further contribute to divergent outcomes across experimental models. Current limitations include incomplete structural characterization, batch-to-batch variability, contamination in crude extracts, and poor reproducibility across in vitro and in vivo systems, all of which restrict translational confidence. Overall, polysaccharide bioactivity is best understood as an emergent property of structure-host-microbiome interactions rather than molecular structure alone. Future advances require standardized structural annotation, harmonized experimental protocols, microbiome-informed study design, and clinical validation to enable predictive and translational applications in functional foods and biomedicine.},
}

@article {pmid42144491,
year = {2026},
author = {Voorhees, PJ and Ponek, RM and Liu, JD and Lai, SK},
title = {A Droplet Digital PCR Assay for Quantification of Bacteriophage Viral Vector Titer and Purity.},
journal = {Annals of biomedical engineering},
volume = {},
number = {},
pages = {},
pmid = {42144491},
issn = {1573-9686},
support = {2013-39274//David and Lucile Packard Foundation/ ; R21AI185808//Division of Intramural Research, National Institute of Allergy and Infectious Diseases/ ; DK007737-30/DK/NIDDK NIH HHS/United States ; },
abstract = {PURPOSE: Bacteriophage (phage)-based vectors offer considerable promise as tools for tuning the microbiome with molecular and genetic precision. However, standardized methods to rigorously characterize phage vectors remain lacking. Here, we present an optimized digital droplet PCR (ddPCR)-based assay for quantifying both the purity and potency of phage vector preparations.

METHODS: We utilized central composite design to develop a ddPCR assay capable of quantifying the number of phage vector capsids packed with the phage vector genome or packed with the transgenic DNA of interest. This assay targets 2 unique DNA barcodes, designed to be biologically inert and maximally orthogonal to existing DNA sequences.

RESULTS: Through stringent optimization, we were able to achieve assay conditions that enable a dynamic range of nearly 3 orders of magnitude and correct for systemic error in the assay. We then show that biological activity assays consistently underestimate transgene-packed vector titers, leading to overestimation of true transduction efficiency, particularly when contamination by genome-packed vectors is high. We further demonstrate how this approach facilitates optimization of vector production conditions and substantially improves the precision and reproducibility of phage vector transduction.

CONCLUSION: Compared to assays of biological activity, this optimized ddPCR assay has improved accuracy and, through design of experiments optimization, high precision (CVs = 5.5 ± 1.3% and 4.5 ± 1.0% for the genome and transgene barcodes, respectively). This assay can be broadly adopted to characterize and quality control vector preparations for various applications.},
}

@article {pmid42144716,
year = {2026},
author = {Shen, Y and Li, Y and Zheng, R and Xia, C and Gundel, PE and Nan, Z and Duan, T},
title = {Arbuscular Mycorrhizal Fungi Dominate Over Maternally Inherited Epichloë Endophytes in Controlling Rhizosphere Processes and Pathogen Resistance.},
journal = {Plant, cell & environment},
volume = {},
number = {},
pages = {},
doi = {10.1111/pce.70613},
pmid = {42144716},
issn = {1365-3040},
support = {32071879//National Science Foundation of China/ ; CARS-22 Green Manure//China Modern Agriculture Research System/ ; },
abstract = {Plant-microbe symbioses form a multi-layered system integrating vertically transmitted Epichloë endophytes, arbuscular mycorrhizal fungi (AMF), and the rhizosphere microbiome, with implications for nutrient acquisition and pathogen resistance. Epichloë endophytes are maternally inherited and may exert priority effects that influence subsequent associations with AMF and root microorganisms, ultimately shaping defensive pathways. Here, we manipulated symbiosis of perennial ryegrass (Lolium perenne) with Epichloë sp. LpTG-3 strain AR37 and the AM fungus Acaulospora delicata to examine exudate metabolites and the recruited rhizosphere microbiome in relation to host responses to the pathogen Bipolaris sorokiniana. Dual symbiosis with Epichloë and AMF increased host growth and pathogen resistance through enhanced nutrient uptake, elevated defensive enzyme activities in leaves and rhizosphere, and reduced malondialdehyde concentrations. It also recruited potentially beneficial microorganisms and enriched metabolites negatively associated with disease severity; notably, the metabolite Acetamide 1, which accumulated under dual symbiosis, strongly inhibited the pathogen in vitro. Significant correlations among metabolites, rhizosphere microbial communities, and rhizosphere soil properties revealed coordinated belowground responses under the synergistic regulation of AMF and Epichloë that reduced disease severity. Although both symbionts enhanced host performance, AMF played a stronger role than maternally inherited Epichloë in shaping the rhizosphere processes driving growth and pathogen resistance.},
}

@article {pmid42144903,
year = {2026},
author = {de Assis, MR and Guimarães, I},
title = {Cholinergic anti-inflammatory pathway and vagus nerve stimulation in rheumatoid arthritis.},
journal = {Current opinion in rheumatology},
volume = {},
number = {},
pages = {},
doi = {10.1097/BOR.0000000000001170},
pmid = {42144903},
issn = {1531-6963},
abstract = {PURPOSE OF REVIEW: To integrate mechanistic and clinical evidence on vagal regulation of immunity via the cholinergic anti-inflammatory pathway, linking neural and inflammatory signaling in rheumatoid arthritis (RA). It highlights how reduced vagal tone contributes to disease onset and progression and frames neuromodulation as a rationale for adjunctive therapeutic strategies.

RECENT FINDINGS: Preclinical and clinical data demonstrate that vagal efferent activity modulates immune responses through noradrenergic circuits and activation of α7-nicotinic-acetylcholine-receptors on immune cells, inhibiting NF-κB nuclear translocation and reducing pro-inflammatory cytokines. This neuroimmune axis interacts with the hypothalamic-pituitary-adrenal axis and the microbiome, supporting an integrated model of inflammation. Vagus nerve stimulation (VNS) has been associated with reductions in inflammatory markers and clinically meaningful improvements in patients with RA. Implantable VNS has demonstrated efficacy and has received regulatory approval for moderate-to-severe RA refractory to disease-modifying antirheumatic drugs; however, the available evidence remains limited and requires confirmation in larger and more diverse populations. Noninvasive approaches show favorable safety profiles but heterogeneous efficacy and currently lack regulatory approval for immune-mediated diseases.

SUMMARY: VNS represents a promising adjunct to conventional immunosuppressive therapy for RA. Further well-designed trials are needed to standardize stimulation protocols, and define optimal strategies for clinical implementation.},
}

@article {pmid42144927,
year = {2026},
author = {Fraser, DR and Mason, RS},
title = {Microbial biosynthesis of vitamin D2.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-21},
doi = {10.1017/S0029665126103073},
pmid = {42144927},
issn = {1475-2719},
abstract = {In the early history of vitamin D research most of the studies on its chemistry and function were performed with vitamin D2 which was readily obtained by UV irradiation of ergosterol from yeast. Yet, in the physiological economy of vitamin D for most vertebrates, including humans, fish and especially for birds, vitamin D3 produced in skin by solar irradiation of 7-dehydrocholesterol, is the natural form of vitamin D. Vitamin D2, as a dietary supplement, while of comparable potency to vitamin D3 in most mammals, has been found in nature only when ergosterol in fungi is inadvertently exposed to solar UV radiation. Nevertheless, some herbivorous animals, horses and elephants, seem to maintain adequate vitamin D status with vitamin D2 rather than vitamin D3. The source of that vitamin D2 has been assumed to be the traces derived from ergosterol in endophytic fungi exposed to the sun on grass being consumed. However, outdoor grazing sheep in winter maintained adequate vitamin D status with vitamin D2, yet no vitamin D2 could be detected on the grass they were consuming. Bovine rumen contents, fermenting in an artificial rumen, had an increase in vitamin D2 concentration, particularly when cellulose fibre was added as a fermentation substrate. Furthermore, mice being raised from weaning on a vitamin D-free diet had vitamin D2 in their colon contents. This review examines anaerobic microbial production of vitamin D2 in the alimentary tract, in the dark, and describes a natural function for vitamin D2 in microorganisms and potentially for gut health.},
}

@article {pmid42145141,
year = {2026},
author = {Sreekumaran, S and V K, P and M N, A and Premnath, M and P S, S and P R, P and Mathew, J and E K, R},
title = {Comparative Human-Poultry Fecal Resistome Profiling from Broiler Farms Reveals Diverse Antimicrobial Resistance Genes.},
journal = {Foodborne pathogens and disease},
volume = {},
number = {},
pages = {15353141261449964},
doi = {10.1177/15353141261449964},
pmid = {42145141},
issn = {1556-7125},
abstract = {Indiscriminate use of over-the-counter antibiotics has led to the rapid emergence of resistant genes in bacteria, with the ultimate crisis to global health. One of the prominent sectors with the antimicrobial resistance (AMR) concern is the farm animals that exist in close contact with humans where the environmental conditions are favorable for the rapid dissemination of pathogenic organisms and resistance genes. Hence, to understand the threat with environmental AMR, a detailed molecular insight is very important. In this study, fecal samples from both poultry and associated humans were studied by metagenomics analysis. From the results, a primary understanding on the microbial diversity difference could be generated from the selected samples. Here, the poultry samples were identified to have more microbial diversity. At the same time, several pathogens were found to be shared commonly between the hosts. Upon detailed examination, several AMR genes were also observed to be common between the poultry and human samples. The results of the study are highly relevant in light of the "One Health" concept where an integrated approach is targeted.},
}

@article {pmid42145228,
year = {2026},
author = {Lischka, J and Weghuber, D and Dinan, TG and Le Roux, CW and Schellekens, H},
title = {Optimizing Adherence and Outcomes: Potential Strategies to Enhance the Effectiveness of nutrient-stimulated hormone therapies.},
journal = {The Proceedings of the Nutrition Society},
volume = {},
number = {},
pages = {1-27},
doi = {10.1017/S0029665126103036},
pmid = {42145228},
issn = {1475-2719},
abstract = {Nutrient-stimulated hormone therapies (NuSH) therapies, a key class within obesity management medications, have reshaped obesity and type 2 diabetes care, producing substantial weight loss, improved glycaemic control, and significant cardiometabolic benefits in adults and adolescents. Yet outcomes vary widely, and NuSH therapy-induced changes in appetite, eating behaviour, and gastrointestinal function can compromise nutrient intake, lean mass preservation, and long-term adherence. This review synthesises evidence across nutrition, behavioural science, microbiota research, and metabolic-bariatric surgery (MBS) to outline supportive strategies that optimise clinical outcomes with NuSHs.Preclinical studies consistently show that NuSH therapies shift gut microbiota toward "lean-associated" profiles, while emerging human findings suggest that baseline microbial signatures may contribute to variability in response and tolerability. However, evidence in humans remains limited, heterogeneous, and underpowered. Across age groups, structured nutritional and behavioural support remains essential to ensure nutrient adequacy, manage side effects, strengthen adherence, and guide sustainable lifestyle change.Key research priorities include defining behavioural and microbial contributors of treatment response and adherence, evaluating microbiota-targeted adjuncts, and developing scalable, multidisciplinary care models for both adult and paediatric populations. NuSH therapies are powerful tools, but their long-term success depends on integrated, personalised nutrition and behavioural care, with growing opportunity for microbiome-informed approaches.},
}

@article {pmid42145481,
year = {2026},
author = {Godoy-Vitorino, F and Méndez-Lázaro, P and Bolaños-Rosero, B and Baerga-Ortiz, A and Torres-Rodríguez, P and Sosa, MA and Vázquez, M and Rivera-Rivera, NL and Cardona-Cordero, N and Colón-López, V and Ortiz, AP},
title = {Environmental exposures, microbiome dynamics and chronic disease risk in climate-vulnerable regions: interdisciplinary perspectives from Puerto Rico.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1807779},
pmid = {42145481},
issn = {2296-2565},
mesh = {Humans ; Puerto Rico/epidemiology ; *Microbiota ; *Environmental Exposure/adverse effects ; Chronic Disease/epidemiology ; *Air Pollution/adverse effects ; *Vulnerable Populations ; },
abstract = {Environmental factors such as air pollution, weather events, and ambient toxins are major contributors to human disease, with disproportionate impacts on vulnerable populations. In Puerto Rico, chronic exposure to air pollution and ecological disruption poses significant public health risks, particularly for cancer and other chronic conditions. These risks are unevenly distributed, disproportionately affecting children and older adults, groups central to community resilience yet highly susceptible to pollution-related health effects. This perspective review synthesizes emerging evidence linking chronic air pollution and environmental exposures to cancer, respiratory and cardiovascular disease, and microbiome alterations that may mediate long-term health trajectories. Drawing on interdisciplinary efforts from the Caribbean Cancer Research Center on Environmental and Natural Hazards, the Center for the Promotion of Cancer Health Equity, the Caribbean Collaborative Action Network, a NOAA CAP/RISA Team, and the Puerto Rico Center for Microbiome Sciences, this paper examines how environmental exposures shape health disparities. We highlight studies demonstrating that fungal spores, particulate matter, and chemical pollutants disrupt microbiome balance, immune regulation, and metabolic pathways, thereby increasing disease risk in early life and aging populations. The review also considers social determinants of health, spatial inequities, infrastructure vulnerabilities, and policy frameworks that influence exposure and resilience. By integrating environmental epidemiology, microbiome research, and public health policy, this synthesis underscores the urgency of planetary health-informed prevention, surveillance, and management strategies to mitigate pollution-related disease burdens, reduce inequities, and strengthen health in climate-sensitive regions globally.},
}

Humans
Puerto Rico/epidemiology
*Microbiota
*Environmental Exposure/adverse effects
Chronic Disease/epidemiology
*Air Pollution/adverse effects
*Vulnerable Populations

@article {pmid42145567,
year = {2026},
author = {Silva, FA and da Silva, RT and Harcourt, N and Biggs, E and Magnani, M},
title = {Indigenous microbiology: Why Indigenous knowledge matters in microbial science.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag024},
pmid = {42145567},
issn = {2633-6685},
abstract = {Indigenous knowledge has long engaged with microorganisms through relationships with environment, food, and health, yet these understandings remain marginal in mainstream microbiology. In this article, we argue that Indigenous microbiology offers a broader framework for microbial science by placing microorganisms within ecological, cultural, and ecosystem-specific relationships. This perspective is relevant to current challenges in sustainable agriculture, food security, and antimicrobial resistance. Drawing on examples from environmental management, traditional fermented foods, and therapeutic practices, we show that Indigenous knowledge can deepen microbiome research and contribute to developing healthy and sustainable strategies. Indigenous microbiology should not be treated as an informal add-on to existing science, but as a valuable framework for asking better questions about microbial life and its role in human and environmental wellbeing.},
}

@article {pmid42145603,
year = {2026},
author = {Waltmann, A and Puerto-Meredith, SM and Chinkhumba, J and Mzembe, E and Kayange, M and Carroll, I and Roach, J and Mathanga, DP and Gutman, JR and Juliano, JJ},
title = {Beyond malaria prevention: sulfadoxine-pyrimethamine treatment in pregnancy selectively remodels the maternal gut microbiome to increase gestational weight gain and improve birthweight.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.03.26352319},
pmid = {42145603},
abstract = {Intermittent preventive treatment in pregnancy (IPTp) with sulfadoxine-pyrimethamine (SP), an antifolate drug with antimalarial and antibiotic activity, reproducibly improves birthweight across sub-Saharan Africa and the Western Pacific. This clinical protection is independent of SP's original malaria indication: it is not diminished by widespread antimalarial resistance or reduced transmission, and SP outperforms more potent non-antibiotic antimalarials (e.g., dihydroartemisinin-piperaquine, DP) for fetal growth. The biological mechanism is unexplained. We previously showed that gestational weight gain (GWG) is a significant component of this mechanism and mediates two-thirds of SP's overall birthweight benefit (NCT03009526). In the first longitudinal characterization of antifolate antibiotic effects on the pregnant gut microbiome, we show that ∼45% of SP's GWG advantage over DP is explained by gut microbial changes consistent with its pharmacology. Microbiome-mediated GWG coincided with 126g higher birthweight in SP but not DP recipients (95%CI 22.6-229.3g; p=0.019). Relative to DP, SP suppressed gastrointestinal pathobionts and enriched anaerobic commensals with recognized roles in mucosal immunity and host metabolism, a microbiome-sparing pattern distinct from conventional antibiotic-associated dysbiosis.},
}

@article {pmid42145647,
year = {2026},
author = {Xing, J and Xu, Z and Zhang, Y and Zhang, H and Zheng, L and Zhang, M and Guo, W and Liu, J and Pan, Y and Zhang, J and Jie, Z and Baele, G and Li, C and D'Souza, A and Zhao, J and Li, J and Chen, T and Wu, H},
title = {Longitudinal cross-species transmission of microbiomes and resistomes across farmers, animals and environment.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.06.26352545},
pmid = {42145647},
abstract = {Understanding the acquisition and dissemination of microbiomes and antimicrobial resistance genes (ARGs) that circulate across human-animal-environment interfaces remains a central One Health challenge, largely because of complex ecological interactions and multiple confounding factors. Although occupational exposure is known to influence the microbiomes and resistomes of farmers, how environmental compartments involve in this system is unclear. Here, we conducted a one-year longitudinal study combining strain-resolved metagenomics (500 metagenomes) with isolate-based whole-genome sequencing (28 isolates) in an ecologically managed, antibiotic-free farming ecosystem spanning animals, farmers, environmental compartments and non-exposed individuals. Assembling 6,075 species-level genomes, we show that animal-associated occupancy reshapes the microbiome and resistome of occupationally exposed farmers and their surrounding environments. Animals and their associated habitats formed the dominant interface for both strain sharing and ARG dissemination across connected ecological compartments, whereas village residents and surrounding river samples - used as ecological controls - showed limited integration into this sharing network. Tracking a frequently shared lineage further revealed within-lineage genetic turnover together with selection-consistent changes following cross-species spread, suggestive of ecological selection across hosts and habitats. Finally, we identify Klebsiella pneumoniae as the most widespread ESKAPE pathogen in this ecosystem, with repeated occurrence across animal, human and environmental compartments, consistent with a neglected but clinically critical broad profile of ecological generalist. Together, these findings identify animals as central interfaces for microbiome and resistome sharing and show how agricultural ecosystems can sustain circulation of opportunistic pathogens and resistance determinants across human-animal-environment interfaces even in the absence of routine antibiotic use.},
}

@article {pmid42145753,
year = {2026},
author = {Wu, Y and Yan, H and Li, P and Liu, Y and Leng, J and Cui, Y and Lv, X and Pang, L and Zang, N},
title = {Bridging the gaps: the gut-lung axis and microbial metabolites in the pathogenesis and treatment of pulmonary fibrosis.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1817835},
pmid = {42145753},
issn = {2296-858X},
abstract = {Pulmonary fibrosis (PF) is a chronic interstitial lung disease characterized by structural damage to the lung parenchyma, excessive deposition of extracellular matrix (ECM), and irreversible decline in lung function. Current pharmacological treatments cannot effectively reverse fibrosis, highlighting an urgent need for novel therapeutic targets. Recently, the gut-lung axis and its bidirectional communication have received increasing attention for their roles in PF progression. Metabolites derived from gut microbiota, including short-chain fatty acids (SCFAs), bile acids, tryptophan metabolites, lipopolysaccharides (LPS), and trimethylamine N-oxide, regulate immune responses, modulate signaling pathways, influence epigenetic modifications, and maintain intestinal barrier integrity, thereby exerting bidirectional effects on PF. Protective metabolites primarily inhibit fibroblast activation and collagen deposition, whereas pathological metabolites promote fibrosis by inducing inflammatory responses and oxidative stress. Potential therapeutic strategies targeting the gut-lung axis include fecal microbiota transplantation (FMT), probiotic and dietary interventions, and Traditional Chinese Medicine (TCM). However, clinical applications face challenges such as donor standardization, immunological safety, and consistency of therapeutic efficacy. Critical limitations remain, including reliance on acute-injury animal models that inadequately represent the chronic, irreversible nature of human PF. Translating findings across distinct PF subtypes requires caution, as their genetic architectures, immune landscapes, and microbiome interactions may differ considerably. Additionally, the causal relationship between microbial dysbiosis and fibrosis remains unclear, and clinical translation currently lacks stratified intervention strategies based on biomarkers. Future research should prioritize large-scale longitudinal cohort studies, integrated multi-omics analyses, organoid models, and gut-lung chip platforms to identify key effector molecules and therapeutic targets, ultimately facilitating precise clinical interventions targeting the gut-lung axis.},
}

@article {pmid42145889,
year = {2026},
author = {McGrath, AH and Steinberg, PD and Kjelleberg, S and Marzinelli, EM},
title = {Effects of Extreme Rainfall on a Dominant Seaweed Are Mitigated by Its Microbiota.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73644},
pmid = {42145889},
issn = {2045-7758},
abstract = {Extreme weather events are becoming more intense and frequent, driving unprecedented ecological changes globally. The effects of such extreme events can be particularly profound if they affect the performance of habitat-forming organisms (trees, corals, kelp). Further, the emergence of the "holobiont" concept in biology suggests that these impacts can occur directly on the habitat-forming "host" and/or via disruption of their associated microbiota. Following a one-in-100 year rainfall event along the coast of Sydney, Australia, we examined the effects of rainfall (in the field) and lowered salinity (in the lab) on the performance and reproductive output of a dominant, habitat-forming intertidal seaweed, Hormosira banksii. We then examined the ability of surface-associated microbes to mitigate host responses to extreme rainfall via microbial manipulations in the field. Extreme rainfall and reduced salinity (< 25 ppt) negatively affected host reproductive output. Manipulative field experiments using a combination of antimicrobial treatments applied once (pulse) or regularly (press) showed that disruption of Hormosira's microbiota after extreme rainfall affected host photosynthesis and, more importantly, inhibited the post-event recovery of host reproductive output. Press disruption of the host-microbiota prevented recovery of normal (control) levels of reproductive output and photosynthesis for over 4 months. These experiments demonstrate that host-associated microbiota can play a significant role in mediating responses of habitat-forming seaweeds to extreme weather events, with consequences for key components of fitness. Given the increased frequency of flooding and storm events experienced by many systems, the microbiome may provide a key role in influencing habitat resilience to stress.},
}

@article {pmid42145945,
year = {2026},
author = {O'Sullivan, E and Solano, O and Oliveira, JS and Johnson, AJ and Dhital, S and S Pillai, PK and Dias, F and Ubbink, J and Lin, AW and Teigen, L},
title = {The food matrix as a confounder in diet‒microbiome studies: methodological challenges and research gaps.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2671724},
pmid = {42145945},
issn = {2993-3935},
abstract = {Interactions of structural and physicochemical properties of food (e.g. texture, viscosity, and solubility), known as the food matrix, are primary drivers of host digestive kinetics. While the impact of matrix-driven variability on nutrient bioaccessibility, glycemic response, and caloric absorption is well documented, these dynamics are often overlooked in diet-microbiome research. Adequately modeling the spatiotemporal availability of microbial substrate is essential to understanding how dietary patterns impact the microbiome throughout the gastrointestinal tract. This narrative review 1) synthesizes current evidence on how food processing and structure affect human digestion and absorption of macronutrients; 2) illustrates how host digestive kinetics impact forms and quantity of substrate delivered and available to the gut microbiota; and 3) identifies challenges and knowledge gaps in current diet-microbiome research regarding food structure. The challenges and knowledge gaps discussed here call for in vivo models that can better model microbial substrate availability throughout the gastrointestinal tract to improve our understanding of diet-microbiome interactions.},
}

@article {pmid42146050,
year = {2026},
author = {Huang, X and Yang, X and Yu, Y and Huang, J and Tao, W and Yu, R},
title = {Bibliometric analysis of human microbiota-associated animal model (2005-2025).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1777297},
pmid = {42146050},
issn = {1664-302X},
abstract = {BACKGROUND: The research on human microbiota-associated (HMA) animal models is an important tool for studying the human microbiome and holds great potential for elucidating disease mechanisms and microbe-based therapeutic interactions. However, a systematic bibliometric assessment of this field has been limited.

METHODS: This study employed bibliometric methods, retrieving relevant publications published between 2005 and 2025 from the Web of Science Core Collection, Scopus, and PubMed, and visualizing the data with VOSviewer and CiteSpace.

RESULTS: The analysis revealed a continuous upward trend in the number of publications on this topic. The United States and its research institutions contributed the most and maintained close collaborations with multiple countries. The majority of the articles appeared in journals such as Gut Microbes, Microbiome, and Proceedings of the National Academy of Sciences of the United States of America (PNAS). Keyword and highly-cited reference analyses focused on the application of these models in investigating disease mechanisms and therapeutic exploration, particularly for metabolic, gastrointestinal, oncological, and neurodegenerative diseases. In addition, the impact of modeling factors such as diet and host genetics on the models has also attracted attention.

CONCLUSION: HMA animal models have become a core platform linking clinical and basic microbiology research, demonstrating unique advantages in recapitulating disease-associated microbial features and phenotypes. Nevertheless, because these models are essential for testing causal links between microbiota and disease, methodological standardization and procedural refinement are needed to enhance reproducibility and clinical applicability.},
}

@article {pmid42146054,
year = {2026},
author = {Li, X and Yu, X and Zhong, Y and Zhou, G and Zou, Y},
title = {Microecological modulators-new perspectives for treating sex hormone disorders.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1795152},
pmid = {42146054},
issn = {1664-302X},
abstract = {Sex hormone related disorders, characterized by complex etiology and long-term health risks, pose a significant challenge to global health. Hormone-based therapies are often accompanied by adverse effects and fail to address the underlying pathophysiological mechanisms. The "gut microbiota-sex hormone axis" maintains endocrine homeostasis through diverse pathways, including enzymatic reactions, immune modulation, metabolic regulation, and the microbiome-gut-brain axis. Dysregulation of this axis has been identified as a critical factor in the pathogenesis of sex hormone-related disorders. Probiotics have emerged as a promising adjunctive therapeutic strategy by targeting this axis. Preclinical and clinical studies have demonstrated that specific probiotic strains ameliorate hormonal imbalances, attenuate inflammation, and optimize metabolic parameters, showing positive efficacy in sex hormone-related disorders. This review systematically elaborates the regulatory mechanisms of this bidirectional axis and highlights the application of probiotics and its regulatory roles as targeted interventions in related disorders.},
}

@article {pmid42146064,
year = {2026},
author = {Sin, J and Choi, D and Hwang, I and Kim, S and Bunch, H and Kim, H and Chung, DK},
title = {Culture supernatants from human-derived commensal bacteria alleviate DNCB-induced atopic dermatitis through modulation of inflammatory and barrier-associated pathways.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1813592},
pmid = {42146064},
issn = {1664-302X},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a chronic inflammatory skin disorder characterized by immune dysregulation, impaired epidermal barrier function, and recurrent episodes of itching and inflammation. Emerging evidence suggests that skin-resident microbiota influence host immune responses and may modulate AD pathogenesis. Here, we investigated the anti-inflammatory, barrier-restoring, and neuro-supportive effects of culture supernatants (CSs) derived from skin-resident bacteria.

METHODS: Human keratinocytes (HaCaT) stimulated with tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ) were treated with CSs from various isolates. For in vivo evaluation, a 2,4-dinitrochlorobenzene (DNCB)-induced AD-like mouse model was utilized, receiving topical applications of the CSs. Furthermore, differentiated SH-SY5Y neuronal cells were treated with keratinocyte- or fibroblast-conditioned media, prepared after stimulation with bacterial CSs, to evaluate their neurotrophic potential.

RESULTS: CSs from Brachybacterium paraconglomeratum and Brevibacterium casei significantly suppressed interleukin-6 (IL-6) and C-C motif chemokine ligand 17 (CCL17) while restoring filaggrin expression. In keratinocytes and human dermal fibroblasts, these CSs increased brain-derived neurotrophic factor (BDNF) expression. In the DNCB-induced AD-like mouse model, topical application of B. paraconglomeratum and B. casei CSs reduced epidermal hyperplasia and immune cell infiltration, downregulated tyrosine hydroxylase (TH), and restored cutaneous BDNF, glial cell line-derived neurotrophic factor (GDNF), and filaggrin (FLG) expression. In differentiated SH-SY5Y neuronal cells, the conditioned media treatments markedly upregulated BDNF, GDNF, and nerve growth factor (NGF). Mechanistically, CS treatment inhibited p38 MAPK and JAK-STAT signaling.

DISCUSSION: Collectively, these findings demonstrate that specific skin-derived bacterial metabolites exert coordinated anti-inflammatory, barrier-reinforcing, and neurotrophic activities, thereby promoting associated changes in neurotrophic markers. Such microbial products may serve as promising biologic candidates for managing atopic dermatitis.},
}

@article {pmid42146065,
year = {2026},
author = {Orwa, P and Kuhl-Nagel, T and Meinhold-Ernst, R and Jehle, JA and Mwirichia, R and Linkies, A},
title = {Linking microbiome structure to functional analysis identifies resilient Pseudarthrobacter, Pseudomonas, and Streptomyces antagonists of Phytophthora infestans in tomato.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1810932},
pmid = {42146065},
issn = {1664-302X},
abstract = {INTRODUCTION: Late blight, caused by Phytophthora infestans, remains one of the most destructive tomato diseases, driving the need for sustainable measures to reduce intensive fungicide use. Plant-associated microbial communities offer a promising but still underexplored source of biological control agents. Moreover, links between community-level microbiome patterns and functionally effective antagonists remain poorly resolved.

METHODS: In this study, we combine culture-dependent isolation, functional profiling of lytic enzymes and siderophores, with 16S rRNA Illumina-based microbiome analysis to identify ecologically relevant bacterial antagonists of P. infestans in tomato. Healthy and P. infestans-challenged tomato plants cultivated in soils from two organic tomato farms in the Rhine-Main region of Germany were analyzed.

RESULTS: Of the 594 bacterial isolates from tomato rhizosphere and phyllosphere, 84 inhibited P. infestans, and 63 of these suppressed Alternaria solani in vitro. Functional screening identified 28 isolates with broad-spectrum antagonistic potential, predominantly affiliated with the genera Pseudomonas, Bacillus, Streptomyces, Paenibacillus, and Pseudarthrobacter, characterized by broad siderophore and taxon-specific lytic enzyme activities. In planta assays identified Pseudarthrobacter sp._Pb177 as a novel and most effective antagonist of P. infestans, alongside effective Streptomyces and Pseudomonas isolates. Amplicon-based microbiome analyses of different tomato compartments under both healthy and P. infestans-challenged conditions revealed soil origin as the primary driver of bacterial community assembly, particularly in the rhizosphere and phyllosphere. Disease-associated shifts were limited to specific soil-compartment combinations (rhizosphere soil B). Key rhizosphere bacterial taxa (Acinetobacter and Chryseobacterium) remained largely stable across plant health states. Instead, disease effects are confined to shifts among rare or conditionally detected ASVs. Mapping cultured isolates to amplicon sequence variants demonstrated that most antagonists corresponded to low-abundance members of the tomato microbiome (including Bacillus, Chryseobacterium, Paenibacillus, Pseudomonas, Streptomyces, etc.), with their distribution shaped primarily by soil and plant compartment rather than disease.

DISCUSSION: These findings indicate that effective biocontrol candidates are defined less by abundance than by their resilience and function within plant-associated microbial communities. By linking microbial community profiling with functional screening and in planta assays, this study outlines a microbiome-informed approach for identifying bacterial antagonists of P. infestans and supports an ecologically grounded framework for managing tomato late blight.},
}

@article {pmid42146066,
year = {2026},
author = {Matsushima, Y and Himi, E and Kitashima, M and Ogura, K and Kotani, S and Hino, A and Inoue, K and Hosoya, H},
title = {A defined synthetic algal medium enables lettuce-free culturing of unfed Paramecium bursaria while preserving host-associated microbiome composition.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821058},
pmid = {42146066},
issn = {1664-302X},
abstract = {Paramecium bursaria is widely cultured using undefined plant-based infusions such as lettuce extract, yet the variable composition of these media remains a major obstacle to experimental reproducibility and microbiome research. Here, we tested whether a chemically defined synthetic algal medium (AF-6) can replace conventional lettuce infusion while maintaining host physiology and associated microbial communities. An unfed clonal strain of P. bursaria, established in 2023 and capable of growth without external nutrient supplementation, proliferated comparably in AF-6 and lettuce media. To confirm that these results were not specific to unfed conditions, we additionally examined a publicly maintained algae-fed strain (NIES-2891), which exhibited similar growth patterns across both media. Cell size, compression-induced extension, and symbiotic algal abundance showed no significant differences between culture conditions. rbcL metataxonomic analysis revealed that Chlorella variabilis was the sole algal endosymbiont detected in all samples. Furthermore, 16S rRNA gene sequencing demonstrated that host-associated bacterial community composition remained largely conserved after replacement of lettuce infusion with AF-6 within each strain, although clear differences were observed between strains. Together, these findings establish an "unfed strain + defined algal medium" framework as a reproducible experimental platform for investigating tripartite interactions among ciliate hosts, symbiotic algae, and associated bacteria.},
}

@article {pmid42146070,
year = {2026},
author = {Chen, C and Shi, Y and Zheng, M and Han, S and Zhang, J and Sun, Z and Yue, Z},
title = {Consecutive monoculture of sweet potato reduces yield due to deteriorated soil health and disrupted nutrient cycling.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1747390},
pmid = {42146070},
issn = {1664-302X},
abstract = {Sweet potato (Ipomoea batatas L.) is a staple food with many promising health benefits. However, obstacles associated with continuous cropping are common in modern intensive sweet potato production, partially due to imbalances in the soil microbiome. This research investigates the succession of the soil microbiome and its impacts following 1, 3, and 5 years of consecutive sweet potato monoculture. The results showed significantly higher diversity and homogeneity in bacteria than in fungi. Although a large proportion of operational taxonomic units (OTUs) were shared, richness analysis indicated a significant decrease in the total number of OTUs for both bacteria and fungi, especially in the fifth year. At the phylum level, Firmicutes and Parcubacteria significantly decreased, while Cryptomycota significantly increased (p < 0.05). Further analysis of the prokaryotic community using BugBase and the Functional Annotation of Prokaryotic Taxa (FAPROTAX) database showed significant changes in many phenotypes and functions. In particular, alterations in human pathogens and Cyanobacteria, as well as differences in carbon metabolism and nitrogen conversion in soils, were revealed for the first time. It was also observed that the contents of soil organic matter (OM), total carbon (TC), and total nitrogen (TN) had a linear correlation with the abundance of Cyanobacteria. However, yield was positively correlated with soil pH but negatively correlated with disease incidence. Taken together, in addition to the distinct succession of the microbial community structure, the study indicates that consecutive monoculture of sweet potato has a significant impact on the health status of soil and nutrient cycling.},
}

@article {pmid42146094,
year = {2026},
author = {Krupa-Kotara, K and León-Guereño, P and Rozmiarek, M},
title = {Editorial: Women's health in an interdisciplinary dimension - determinants of nutritional disorders: Volume II.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1844748},
doi = {10.3389/fnut.2026.1844748},
pmid = {42146094},
issn = {2296-861X},
}

@article {pmid42146321,
year = {2026},
author = {Leyshon, C and Leyshon, M and Esmene, S and Leyshon, M and Clabburn, O},
title = {The Challenges Facing VCFSEs in Integrated Care Systems: A Qualitative Case Study of a Unitary Authority in England.},
journal = {International journal of integrated care},
volume = {26},
number = {2},
pages = {9},
pmid = {42146321},
issn = {1568-4156},
abstract = {INTRODUCTION: Integrated Care Systems (ICSs) in England seek ever-closer collaborative relationships between health and social care providers, local authorities, and the Voluntary, Community, Faith and Social Enterprise (VCFSE) sector to deliver public services in place. However, ICSs present significant challenges for VCFSEs.

METHODS: In-depth qualitative case study of VCFSEs in an ICS contiguous with a Unitary Authority in England.

RESULTS AND DISCUSSION: i) the role of the 'microbiome' of smallest VCFSE in the ICS is unclear; ii) current commissioning models work against the effective participation of VCFSEs in ICSs; iii) short-term and under-funded contracts threaten VCFSEs; iv) substitution and appropriation represent tangible threats to VCFSEs through increased demand and bureaucratisation; v) the degree to which ICS support a vibrant, heterogeneous, and sustainable VCFSE sector depends on 'system maturity'.

CONCLUSIONS: Integration is a process, not an event. The evolving landscape of service design presents both opportunities and challenges for VCFSEs, requiring careful management to harness strategic advantages while addressing operational risks.},
}

@article {pmid42146396,
year = {2026},
author = {Mitchener, MM and Anderson, CM and Veleba, M and Teo, K and Roch, M and Chen, R and Yuan, Y and Han, I and Dziergowska, A and Pethe, K and Begley, TJ and Kline, KA and Dedon, PC},
title = {Growth-dependent tRNA Reprogramming and Codon Bias Link Translation to Metabolic State in Enterococcus faecalis.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.07.723122},
pmid = {42146396},
issn = {2692-8205},
abstract = {UNLABELLED: Enterococcus faecalis is a Gram-positive commensal bacterium of the human gut microbiome and an opportunistic pathogen responsible for many hospital-acquired infections. Despite the clinical importance of E. faecalis , how gene and protein expression are coordinated with growth remains poorly defined. Here, we profiled transcript, protein, and tRNA pool dynamics across distinct phases of E. faecalis growth. Differences in protein abundance and corresponding mRNA levels suggested growth phase-dependent posttranscriptional regulation. Growth-associated genes exhibited biased synonymous codon usage, with ribosomal and glycolytic proteins enriched in low-abundance codons read by queuosine-modifiable tRNAs. Analysis of tRNA modification and tRNA isoacceptor abundance revealed growth phase-dependent changes, particularly in anticodon stem loop modifications that influence synonymous codon translation. Changes in queuosine levels preceded shifts in ribosomal proteins, suggesting a contribution to codon-biased translation. Collectively, these findings reveal growth phase-associated remodeling of the E. faecalis tRNA pool and support a model in which queuosine-dependent translational reprogramming shapes protein expression during bacterial growth.

IMPORTANCE: Enterococcus faecalis is a common cause of hospital-acquired infections. Despite its clinical importance, a comprehensive understanding of the organism's physiology and adaptation to environmental changes remains incomplete. Here, we characterized protein, transcript, and tRNA dynamics across bacterial growth phases, uncovering a role for post-transcriptional regulation marked by tRNA reprogramming and biased synonymous codon usage. These findings enhance our understanding of E. faecalis growth and support a model of translational reprogramming therein.},
}

@article {pmid42146479,
year = {2026},
author = {Haran, V and Wang, J and Morimoto, M and Wong, WM and Rouyer, LSF and McDonald, JG and Meeks, JP},
title = {Bile acid chemosensation in mammals supports species and gut microbiome evaluation.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.30.721772},
pmid = {42146479},
issn = {2692-8205},
abstract = {UNLABELLED: The rodent accessory olfactory system (AOS) detects chemosignals emitted by conspecifics and other species to support beneficial behaviors. Peripheral vomeronasal sensory neurons (VSNs), the AOS' chemical sensors, detect fecal bile acids in patterns that have unknown significance to the animal. We used a combination of mass spectrometry and VSN calcium imaging to investigate the AOS' capacity to use bile acid information to discriminate between fecal samples from captive reptiles and mice with varying gut microbiome states. Mass spectrometry analysis revealed bile acid patterns that distinguished biologically relevant samples from one another, representing theoretical discrimination axes. We measured VSN response patterns to bile acid stimuli aligned with theoretical discrimination axes. We found that VSNs perform stimulus "whitening" via an inverse relationship between natural bile acid abundance and population response magnitude. VSNs showed maximum sensitivity to taurine-conjugated bile acids, which have high theoretical discriminatory value, but were found at low natural abundance levels. Individual taurine-conjugated bile acids drove threat assessment behavior when added to familiar mouse fecal extracts, suggesting high behavioral significance. Finally, we analyzed the degree to which the AOS utilizes the theoretical information about species, diet, and gut microbiome status from bile acids. We found that VSN tuning patterns align with theoretical axes for discriminating reptilian predators from vegetarians, and between mice with different gut microbiome states. VSN tuning was especially well-aligned with the information available about conspecific gut microbiome status. These results show that AOS bile acid chemosensation supports discrimination of multiple biologically relevant states.

SHORT ABSTRACT: The rodent accessory olfactory system (AOS) detects fecal bile acids via combinatorial codes with unknown biological significance. We investigated whether AOS bile acid chemosensation supports species and gut microbiome evaluation using mass spectrometry, calcium imaging in vomeronasal sensory neurons (VSNs), and analytical modeling. Bile acid excretion patterns theoretically supported discrimination of reptilian predators from vegetarians, and germ-free mice from conventionally raised counterparts. VSNs demonstrated stimulus "whitening" via an inverse relationship between natural bile acid abundance and population response magnitude. VSNs had highest sensitivity to taurine-conjugated bile acids, a novel class of chemosignals that elicited behavioral aversion. VSN tuning aligned with ideal discrimination axes, which was especially strong for gut microbiome-associated bile acid abundance patterns. These results show that AOS bile acid chemosensation supports discrimination of multiple biologically relevant states.},
}

@article {pmid42146481,
year = {2026},
author = {Jensen, O and Hanson, L and Hénault, M and Haskins, BE and Trujillo, E and Brown, C and Brunetti, T and McCabe, M and Russo, BC and Heasley, L and Ost, KS},
title = {A Candida glabrata adhesin-like effector drives fitness and immunogenicity in the gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.04.722752},
pmid = {42146481},
issn = {2692-8205},
abstract = {Candida glabrata is a leading cause of invasive candidiasis. The gut serves as its primary reservoir, yet factors governing colonization and pathogenic potential remain poorly defined. Here, we identify immunoglobulin A (IgA) as a key regulator of C. glabrata within the intestinal microbiome. We found that C. glabrata induces an IgA response in a strain-specific manner. Comparative transcriptional and proteomic analyses of IgA-inducing and non-inducing strains identified a putative adhesin, Awp11, whose expression correlated with IgA induction. Awp11 is directly targeted by IgA and is required for inducing C. glabrata -specific IgA and Th17 responses in vivo. Functionally, Awp11 promotes colonization of a complex intestinal microbiome, and intestinal IgA limits this advantage. In most strains, AWP11 transcription is dynamic and limited by IgA in the gut. This identifies Awp11 as a key determinant of strain-dependent immunogenicity and gut colonization that C. glabrata may dynamically regulate to balance colonization and immune evasion.},
}

@article {pmid42146533,
year = {2026},
author = {Steininger, HM and Iglesias-Aguirre, CE and Panzer, AR and Durack, J and McKean, M and Cabana, MD and Diamond, S and Lynch, SV},
title = {Carbohydrate Metabolism Differs in Infants by Asthma-risk Status and is Associated with the Functional Potential of Bacteroides cellulosilyticus.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.721144},
pmid = {42146533},
issn = {2692-8205},
abstract = {Childhood atopic disease is linked to delayed gut microbiome development and metabolic dysfunction, however microbial drivers remain unclear. To explore microbial correlates of asthma risk during a time of active gut microbiome development, we analyzed stool from 6-month-old infants at high asthma risk (HR) or healthy controls (HC), using Genome-resolved metagenomics (HR=7; HC=12) and untargeted metabolomics (HR=11; HC=15). We recovered 82 bacterial species-level metagenomic-assembled genomes (MAGs). Global Taxonomic composition did not differ by asthma risk. Anticipating that key differences might associate with specific genomes, a machine-learning approach pinpointed Bacteroides cellulosilyticus, Hungatella effluvii, and Enterocloster aldenensis as linked with asthma risk status. All three species were more abundant in HC infants and the B. cellulosilyticus genome was enriched for carbohydrate metabolism genes relative to other MAGs. Metabolomic profiling revealed variance associated with asthma risk (PERMANOVA, R2=0.069, p=0.016). HR fecal metabolomes were enriched in simple sugars, whereas HC contained more nitrogenous compounds. Integrative genome-metabolic modeling of compounds that significantly differentiate asthma-risk groups revealed risk-dependent interactions with community-encoded metabolic potential (CEP), for arabinose and agmatine, whose fecal concentrations are linked with B. cellulosilyticus and H. effluvii functional traits respectively. These findings suggest that microbial-influenced metabolic differences associate with asthma risk at 6 months, with B. cellulosilyticus and H. effluvii emerging as candidate bacteria influencing this observed metabolic remodeling.},
}

@article {pmid42146538,
year = {2026},
author = {Yengo, CK and Liu, X and Langley, RJ and Avila, F and Sagar, M and Ochsenbauer, C and Bensing, BA and Hioe, CE},
title = {HIV-1 interactions with sialic acid-binding bacterial lectins promote virus infectivity in vitro and mucosal transmission in humanized mice.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.05.05.722898},
pmid = {42146538},
issn = {2692-8205},
abstract = {UNLABELLED: Most HIV-1 transmission occurs at mucosal surfaces, which are colonized by the host microbiota. However, interactions between HIV and bacteria or bacterial products derived from the human microbiome are poorly characterized, and their biological consequences are largely unexplored. Here, we evaluated the effects of sialic acid-binding lectins expressed by bacterial species ubiquitous in the human microbiota on HIV-1 infectivity using viruses produced in 293T cells and human primary cells. We demonstrated that these bacterial lectins enhanced HIV-1 infectivity in a sialoglycan-dependent manner. Specifically, Siglec-like binding region lectins (SLBR-N, SLBR-H, and SLBR-B) from Streptococcus gordonii and Staphylococcal superantigen-like lectins (SSL3, SSL4, and SSL11) from Staphylococcus aureus increased HIV-1 infectivity to varying extents, depending on lectin type and virus strain. Among these lectins, SLBR-N exhibited the greatest potency, corresponding with its superior ability to bind virions and promote virus-cell attachment. This enhancing activity was observed for direct infection of TZM-bl reporter cells and primary CD4+ T cells, as well as trans-infection in the presence or absence of the mannose-binding host lectin DC-SIGN. Importantly, these findings were corroborated in vivo using humanized mice, in which pre-exposure to SLBR-N promoted rectal HIV-1 transmission and increased viral burdens in plasma and splenic cells. Collectively, the data show sialoglycan-binding bacterial lectins as microbial factors that can enhance HIV-1 transmission at mucosal surfaces, highlighting a potential direct role for the microbiota in modulating HIV-1 acquisition risk.

AUTHOR SUMMARY: HIV is commonly transmitted from one person to another across mucosal surfaces, such as those lining the genital and rectal tracts, which are densely populated by bacteria that make up the human microbiota. Yet, surprisingly little is known about how these bacteria and the molecules they produce influence HIV infection. In this study, we investigated a group of bacterial proteins known as sialic acid-binding lectins that are expressed by common members of the human microbiome: Siglec-like binding region lectins from Streptococcus gordonii and superantigen-like lectins from Staphylococcus aureus . Using multiple HIV strains and several types of target cells, we demonstrate that lectin binding to HIV can increase virus attachment to target cells and thereby enhance infection, although the magnitude of this effect varies among lectins and virus strains. Lectin binding also facilitates HIV spread from cell to cell and promotes mucosal HIV infection in a humanized mouse model, resulting in a higher viral burden in the blood and tissues. These findings identify bacterial lectins as important factors that can influence HIV infection and implicate a potential role for the human microbiota in determining susceptibility to HIV infection.},
}

@article {pmid42146631,
year = {2025},
author = {Madaan, T and Nieman, ML and Rakheja, T and Siddiqui, N and Gherardini, D and Sertorio, M and Kamble, NS and Thomas, SC and Hartman, A and Koch, SE and Knipper, L and Marino, VA and Sadayappan, S and Lorenz, JN and Konhilas, JP and Kotagiri, N},
title = {Modulating Cardiac-Gut Microbiome Interaction Post-Myocardial Infarction with Engineered Bacteria.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.1101/2025.07.10.664025},
pmid = {42146631},
issn = {2692-8205},
abstract = {The gut microbiome plays a critical role in the pathophysiology of acute myocardial infarction (MI). MI events significantly impact intestinal integrity which results in leakage of bacterial products into the systemic circulation. We demonstrate that MI not only compromises intestinal integrity, leading to systemic leakage of bacterial products like LPS, but also results in the translocation and colonization of live, intact gut bacteria in the MI heart - a novel aspect of the heart-gut axis. Our initial findings with natural murine gut microbiome were substantiated using orally administered E. coli Nissle 1917 (EcN), as a tracer bacterium. Furthermore, we engineered EcN to express the microbial anti-inflammatory molecule (MAM) derived from the probiotic Faecalibacterium prausnitzii . Treatment with this engineered strain, EcN-MAM, led to significantly improved survival and cardiac function in MI mice. This was attributed to enhanced gut barrier integrity, resulting in reduced systemic bacterial permeation and subsequent inflammation. These findings shed light on a previously unrecognized dimension of the heart-gut axis and highlight the potential of microbiome-based interventions in MI management.},
}

@article {pmid42146777,
year = {2026},
author = {Mikulikova, I and Lepkova, Z and Bandouchova, H and Blahova, J and Papezikova, I and Novotna, H and Toulova, I and Kobelkova, K and Odehnalova, K and Postulkova, E and Radojicic, M and Mares, J and Mudronova, D and Palikova, M},
title = {The effect of Lactiplantibacillus plantarum probiotic supplement on rainbow trout challenged with Aeromonas salmonicida.},
journal = {Veterinarni medicina},
volume = {71},
number = {4},
pages = {156-168},
pmid = {42146777},
issn = {0375-8427},
abstract = {Two probiotic (Lactiplantibacillus plantarum) supplementation strategies (continuous and cyclic) were evaluated for their ability to enhance resistance of rainbow trout (Oncorhynchus mykiss) to Aeromonas salmonicida infection. Neither of these strategies improved post-challenge survival. Instead, cyclic administration resulted in a significantly higher mortality rate (73%) compared with continuous supplementation (52%) and the control group (46%). One week post-challenge, most haematological, plasma biochemical, and immune parameters showed no significant difference between treatments, though fish receiving cyclic supplementation did exhibit a reduced lymphocyte count. However, three weeks post-challenge, this same group showed a significant decrease in total phagocyte number and in the proportion of phagocytes within white blood cells. IgM concentrations were significantly lower in both probiotic-supplemented groups than in the control group. In the cyclic group, reductions in interleukin-10 and elevations in total protein levels were also observed. Microbiome analysis of gut content three weeks post-challenge revealed a marked decline in microbial diversity in both probiotic-treated groups. These findings indicate that, under the experimental conditions, probiotic supplementation did not provide protection against A. salmonicida infection and that cyclic administration may disrupt immune homeostasis and intestinal microbial stability, ultimately compromising host resilience.},
}

@article {pmid42146906,
year = {2026},
author = {Orletskaia, VA and Olekhnovich, EI},
title = {Ecological and Functional Stratification of the Stool Microbiome Predicts Response to Immune Checkpoint Inhibitors across Cancer Types.},
journal = {Computational and structural biotechnology journal},
volume = {35},
number = {1},
pages = {0065},
pmid = {42146906},
issn = {2001-0370},
abstract = {Despite the recognized role of the gut microbiome in modulating immune checkpoint inhibitor efficacy, the ecological principles governing this relationship remain elusive. Moving beyond cataloging specific bacteria, we investigated whether general ecosystem properties determine clinical outcome. Through genome-resolved metagenomic analysis, we constructed a comprehensive catalog from 951 stool metagenomes and subsequently analyzed a curated subset of 624 samples from 11 multicancer cohorts, with melanoma (72.7%, n = 456) and other cancer types collectively accounting for 27.3% (n = 171), including gastrointestinal, non-small-cell lung, breast, ovarian, and other types. Our catalog comprises 3,816 operational genomic units and reveals the key ecological determinants of immune checkpoint inhibitor response. Clinical benefit was associated with gut ecosystems dominated by prevalent, autochthonous taxa. Indeed, the population frequency of a taxon was a positive predictor of its favorable outcome association. Functionally, responder-associated microbes were enriched in genomic capacity for complex carbohydrate metabolism, including specialized mucin degradation and amino acid biosynthesis. In contrast, nonresponse was characterized by enrichment of low-prevalence, exogenous oral and food-derived bacteria and enriched for replication-associated pathways. Our results support an ecological interpretation of the "Anna Karenina principle" in microbiomes: response is linked to a stable, functionally coherent microbial community, whereas nonresponse represents a destabilized state with high individual variability. This reframes the search for biomarkers from individual taxa to the assessment of ecosystem stability and functional coherence, providing a foundation for microbiome-targeted strategies to improve cancer immunotherapy outcomes.},
}

@article {pmid42147140,
year = {2026},
author = {Vincent, SA and Devlin, PF},
title = {Fungicides disrupt total and endophytic phyllosphere bacterial communities but a salicylic acid hyperimmune mutant shows microbiome resilience.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag102},
pmid = {42147140},
issn = {2730-6151},
abstract = {Stable colonization of plants by beneficial microbes enhances disease resistance, nutrient uptake, and stress tolerance. Disruption of these communities often reduces plant fitness. The phyllosphere microbiome is especially vulnerable to agrochemicals. In this study we examined how synthetic fungicides affect the phyllosphere bacterial community of Arabidopsis thaliana. Application of several widely-used fungicides led to a pronounced decrease in bacterial diversity and depletion of beneficial taxa in both surface and internal leaf microbial communities. Moreover, these microbial responses were influenced by the host plant's genetic background. We previously showed that the phyllosphere microbiomes of plants exhibiting heightened salicylic acid-driven immune responses are enriched in xenobiotic degradation traits. We, therefore, examined whether the disrupted phyllosphere of one such line, the fhy3 far1 mutant, is buffered against fungicide-induced dysbiosis. The fhy3 far1 mutant showed reduced fungicide-induced microbiome disruption in both surface and endophytic microbiomes across both systemic and contact fungicides, supporting the hypothesis that innate plant immunity may help buffer against collateral damage from chemical treatments. Our identification of fungicide-resilient microbial taxa holds promise for the development of next-generation biostimulant products and, additionally, our findings raise the possibility that salicylic acid-mediated immunity could be strategically leveraged as a complementary tool alongside traditional fungicides.},
}

@article {pmid42147160,
year = {2026},
author = {Turnbaugh, P and Zhang, S and Buttimer, C and Trepka, K and Lam, K and Hernandez, LR and Noecker, C and Soto-Perez, P and Canigiula, P and Ortega, E and Lee, J and Ramirez, L and Partipilo, G and Lawrence, H and Bottacini, F and Shkoporov, A and Draper, L and Ross, RP and Coffey, A and Hill, C},
title = {Eggerthella lenta evades bacteriophage through reversible megabase-scale inversions of capsular polysaccharide gene clusters.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9488777/v1},
pmid = {42147160},
issn = {2693-5015},
abstract = {Bacteriophages are a promising tool for microbiome editing, yet their development has been constrained by limited insights into bacteriophage-host interactions within their shared mammalian body habitat. We isolated a lytic phage ΦKL11 that efficiently targets a disease-associated member of the human gut microbiota, Eggerthella lenta , during in vitro growth. However, ΦKL11 selects for a pre-existing and reversible bacteriophage-resistant sub-population in mice. Long-read sequencing revealed a massive genomic inversion event, representing >50% of the E. lenta genome, enriched in response to bacteriophage infection. Transcriptomics linked this inversion to the altered expression of three capsular polysaccharide synthesis (CPS) gene clusters and transmission electron microscopy confirmed differential capsule production. Finally, we show that ΦKL11 has a broad host range attributable to CPS and other strain-variable genes. These findings suggest a previously unrecognized strategy for phage evasion in the gut, involving megabase-scale genomic inversions and reversible capsule variation driving phage resistance.},
}

@article {pmid42147173,
year = {2026},
author = {Ng, J and Trannguyen, J and Wilkinson, R and Conard, F and Fehrenback, S and Ebersole, B and Ghosh, D and Apewokin, S},
title = {Conditioning chemotherapy exposure is associated with epigenetic modifications in Clostridioides difficile isolates from stem cell transplant recipients.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-8865869/v1},
pmid = {42147173},
issn = {2693-5015},
abstract = {Clostridioides difficile is a highly methylated organism within the gut microbiome that is responsible for Clostridioides difficile infection (CDI), a common disease that is mediated by toxins production from the bacterium. C. difficile infection is ten times more common in chemotherapy patients than the average patient, but the reasons for this disparity are unclear. Conditioning chemotherapy (CC), an integral part of cancer treatments, has the ability to induce methylation changes in many cell types. We posit that CC induces methylation changes within C. difficile that may promote toxin production and consequently CDI. To test our hypothesis, we sought to identify the epigenetic changes, particularly methylation changes, within C. difficile isolates before and after chemotherapy and within isolates that express toxin and isolates that do not. After stool sampling, we isolated C. difficile by culture then sequenced and created a hybrid assembly of each isolate using nanopore long read sequencing and Illumina short read sequencing. Bioinformatics tools such as Dorado and Samtools were used to basecall and determine methylation states, while Unicycler was used for genome assembly. Methylartist was then used for data visualization. Genome-wide methylation profiling revealed distinct epigenetic signatures in Clostridioides difficile associated with toxin expression and chemotherapy exposure. Whole-genome 6mA analysis demonstrated significant differences between toxin-positive and toxin-negative isolates, with prominent methylation changes in tcdA and tcdE , while selected sporulation genes were unmethylated in toxin-negative strains. Chemotherapy was associated with a significant shift in global 6mA methylation patterns. Targeted 5mC analysis of the pathogenicity locus revealed reduced methylation around tcdB and across multiple toxin genes following chemotherapy, whereas sporulation genes remained unaffected. These findings suggest chemotherapy-associated epigenetic remodeling of toxin-associated loci in C. difficile .},
}

@article {pmid42147178,
year = {2026},
author = {Gough, E and Basu, S and Brubaker, J and DeNeraing, B and Sack, D and Bourgeois, AL and Walker, R and Harro, CD and Chakraborty, S},
title = {Influence of Gut Microbiota on Immune Responses and Protection in Volunteers Receiving the Live Attenuated Oral ETEC Vaccine ACE257 followed by Virulent ETEC H10407 Challenge.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9284363/v1},
pmid = {42147178},
issn = {2693-5015},
abstract = {Enterotoxigenic Escherichia coli (ETEC) remains a major cause of diarrheal morbidity with no licensed vaccines. Role of gut microbiota in vaccine immunogenicity and protection was investigated using 16S rRNA sequencing from the stool samples of 27 volunteers receiving two doses of the live attenuated oral ETEC vaccine ACE527 followed by virulent ETEC H10407 challenge. Systemic and mucosal IgG and IgA responses to heat-labile toxin-B (LTB) and colonization-factor-antigen-I (CFA/I) were quantified by ELISA in serum and antibody-in-lymphocyte-supernatant (ALS). Microbiome α-diversity, β-diversity, and taxa-immune associations were evaluated using regression models, MiRKAT, and relaxed LASSO. Vaccination increased (~ 25-30%) Eubacterium_brachy_group, Family_XIII_AD3011 and Actinomyces. Higher α-diversity (inverse-Simpson) was associated with reduced ALS anti-LTB and CFA/I IgA responses, whereas β-diversity correlated with increased serum anti-CFA/I IgA. Members of Anaerovoraceae, Peptostreptococcaceae, Oscillospiraceae, and Veillonellaceae enhanced immune responses and protection against severe diarrhea and ETEC colonization, while Ruminococcaceae, Sutterellaceae, Coriobacteria, Clostridia, and Actinobacteria showed antagonistic associations.},
}

@article {pmid42147179,
year = {2026},
author = {Belger, C and Wirbel, J and Maghini, D and Carstens, N and van Coller, A and Beasley, JC and Melzheimer, J and Berkman, AY and Strauss, WM and Hetem, RS and Hazelhurst, S},
title = {The Gut Microbiome Profile of Lions in EtoshaNational Park, Namibia.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9092464/v1},
pmid = {42147179},
issn = {2693-5015},
abstract = {Background: The gut microbiome plays a crucial role in carnivore ecology, diet, and health, yet remains poorly characterised in African lions (Panthera leo melanochaita). Previous studies of lion microbiomes have primarily focused on small numbers of captive individuals maintained on controlled diets of Asian origin, reporting Fusobacteriota and Firmicutes as dominant phyla. Some recent literature has begun to describe microbiome composition in free-living African lions; however, genome-resolved analyses and detailed functional characterisation of the wild African lion gut microbiome remain lacking. Results: We present the first comprehensive gut microbiome analysis of free-living African lions, including novel MAGs generated from examining 23 fresh faecal samples from 20 individuals in Etosha National Park, Namibia. The African lion gut was dominated by Bacteroides (22.1%) and Phocaeicola (13.3%) - two related genera - contrasting sharply with the captive lions where Fusobacterium (Bhopal, India) and Firmicutes (Rotterdam, Netherlands) predominate. This divergence likely reflects dietary differences, captivity effects and possibly allopatric separation. While recent work has begun to characterise taxonomic composition in wild African lions, our study extends these findings through the reconstruction of 318 bacterial and 102 viral metagenome-assembled genomes (MAGs) from combined short- and long-read sequencing data. Most MAGs shared <95% average nucleotide identity with existing reference genomes, indicating largely novel species. Supplementing the GTDB database with these MAGs reduced unclassified reads from 24.5% to 9.2%, demonstrating the substantial gaps in existing carnivore gut microbiome databases. Functional analysis revealed metabolic pathway enrichment, particularly for purine metabolism-critical for processing the lions' high-purine diet-with nearly complete pathways for degrading adenine and guanine to urea. Conclusions: This study provides the first in depth description of the microbial taxa in the African lion gut microbiome. Genera in the Bacteroidaceae family dominated. There are large differences with the metagenomics of the n = 3, 4 hybrid and Asiatic lions on controlled diets reported in prior studies. The discovery of over 300 novel MAGs significantly expands microbial reference databases and underscores the unique and understudied nature of apex carnivore microbiomes. These findings show critical microbial contributions to carnivore nutrition and establish a foundation for microbiome-based approaches to wildlife health monitoring and conservation management of threatened lion population.},
}

@article {pmid42147183,
year = {2026},
author = {Topacio, TM and Maltz, MR and Lo, DD and Zaza, M and Porter, WC and Freund, L and Lyew, A and Cocker, D and Biddle, T and Yisrael, K and Castillo, DD and Dingilian, H and Drover, RW and Botthoff, J and Aronson, E},
title = {Chronic exposure to Salton Sea aerosols elicits pulmonary inflammation and shifts in murine lung and fecal microbiome diversity.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9569949/v1},
pmid = {42147183},
issn = {2693-5015},
abstract = {Lung disease is rampant around the Salton Sea, California's largest inland lake and a major source of airborne particulates. To examine root causes of pulmonary disease, we investigated the exposure impacts of spatiotemporal variation in aerosols collected near the Salton Sea on lung and fecal microbiomes. We collected dust during the summer and fall at three different sites around the Salton Sea from 2020 to 2022. Dust was filtered to remove microbial cells and aerosolized for 7-day chronic murine exposures within controlled environmental chambers, after which mouse lung and fecal samples were used for 16S rRNA V3-V4 amplicon sequencing. We verified that chronic exposure to aerosols elicits neutrophilic pulmonary inflammation, particularly in mice exposed to collections from the Wister site near the Salton Sea. We found that spatiotemporal variation drove variation in lung microbiome composition in mice exposed to aerosols from 2022. The lung microbiomes of Salton Sea aerosol-exposed mice were found to increase in alpha-diversity and richness, while simultaneously decreasing in evenness. In contrast, the fecal microbiomes of aerosol-exposed mice decreased in diversity and richness. Our findings suggest that chronic exposure to aerosols from Wister, a site immediately Southeast of the Salton Sea, triggers a systemic stress response in mice characterized by high pulmonary neutrophil recruitment, increased lung microbiome diversity, and decreased fecal microbiome diversity. Back trajectory analyses for aerosol surface type frequencies revealed higher contributions from the Salton Sea in 2020 and 2022 collections from Wister. These findings suggest that chronic exposure to Salton Sea aerosols have impacts on host pulmonary and systemic health, as emphasized by significant but opposing effects on lung and fecal microbiome diversity. Furthermore, these findings demonstrate the variable capacity of environmental aerosol exposure to elicit health consequences relative to seasonal weather events.},
}

@article {pmid42147187,
year = {2026},
author = {Caspi, R and Zhang, A and Horai, R and Jittayasothorn, Y and Badger, J and Wu, Z and Shi, G and Gupta, A and Arunkumar, S and Murphy, C and Nagarajan, V and McCulloch, J and Kodati, S and Sen, H and Lee, JW and Jacobs, J and Xu, X and Mattapallil, M and Peng, Z and Xu, B and Palmer, R and Majdalani, N and Honda, K and O'hUigin, C},
title = {Gut microbial interaction networks control autoimmunity to neuroretina.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9528424/v1},
pmid = {42147187},
issn = {2693-5015},
abstract = {The gut microbiome influences the development of immune-mediated inflammatory diseases, including autoimmune uveitis, a sight-threatening ocular inflammation driven by retina-specific T cells1. Using a model of spontaneous autoimmune uveitis (sEAU) we showed that gut commensals provide immune stimuli that trigger disease2. Here we report that uveitis-promoting microbes are present in human gut flora and that colonization of germ-free (GF) mice with commensals from healthy human donors was sufficient to provoke disease. Severity of sEAU correlated with expansion of Akkermansia and contraction of short-chain fatty acid (SCFA)-producing Firmicutes, followed by decreased SCFA levels and a dominant gut Th1 effector response. Mechanistic gain-of-function experiments, enriching GF sEAU mice with Akkermansia, reproduced these microbiome, metabolite and immune phenotype shifts, and exacerbated disease, suggesting that Akkermansia promotes autoimmunity by outcompeting SCFA-producers and enhancing Th1-type responses. An inverse correlation between Akkermansia (Verrucomicrobia) and Firmicutes was also present in patients with uveitis, multiple sclerosis and Crohn's disease. These findings reveal a stereotypic gut microbial interaction network that regulates systemic immune balance, and may represent an ecologically conserved mechanism through which the gut microbiome modulates autoimmune and inflammatory diseases.},
}

@article {pmid42147198,
year = {2026},
author = {Lewis, K and Patil, P and Liang, HW and Astley, E and Taher, R and Lee, MH and Norment, D and Iinishi, A and Gupta, N and Sobolevskaia, K and Chen, E and Nawab, A and Adzre, J and Moss, C and Hawkins, B and Bourgeois, J and Caimano, M and Brissette, C and Hu, L},
title = {A deformylase inhibitor expands therapeutic options for Lyme disease.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9335039/v1},
pmid = {42147198},
issn = {2693-5015},
abstract = {Lyme disease incidence continues to rise globally. This vector-borne infection remains a major public health burden. Broad-spectrum doxycycline and ceftriaxone disrupt the gut microbiome, drive resistance in commensals, and offer suboptimal efficacy against neuroborreliosis. Here we show that forazemin, previously known as BB-83698, is an orally bioavailable peptide deformylase inhibitor with potent and selective bactericidal activity against spirochaetes, including diverse Borrelia species. Targeting the deformylation of nascent peptides, forazemin halted protein synthesis, thereby killing the spirochaetes. In murine models of Lyme borreliosis and neuroborreliosis, short oral dosing regimens cleared infection, and forazemin was more effective than doxycycline in tick-bite prophylaxis. Forazemin preserved microbiome diversity and spared beneficial gut symbionts. These findings support forazemin as a candidate for the treatment and prevention of Lyme disease.},
}

@article {pmid42147301,
year = {2026},
author = {Barbosa, MC and Pellegrinetti, TA and da Cunha, ICM and da Silva, AVR and Marcandalli Boleta, EH and Losovoi, LA and Mendes, R and Tsai, SM and Mendes, LW},
title = {Genotype-dependent stability and specialization of arbuscular mycorrhizal fungal communities under drought in common bean.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1786322},
pmid = {42147301},
issn = {1664-462X},
abstract = {Arbuscular mycorrhizal fungi (AMF) represent a key biological strategy for enhancing agricultural resilience under extreme climatic events such as drought. However, how AMF interact with drought-tolerant plant genotypes to sustain performance under water limitation remains poorly understood. Here, we used high-throughput DNA sequencing to investigate AMF communities associated with drought-tolerant (BAT477 and SEA5) and drought-susceptible (IAC-Milênio and IAC-80SH) common bean genotypes, integrating taxonomic, structural, and functional perspectives under contrasting water regimes. We hypothesized that drought tolerance is not simply linked to AMF presence, but rather to the ability of host genotypes to structure and stabilize their mycorrhizal communities under stress. Our results reveal genotype-specific responses to drought, with distinct community restructuring dynamics observed across individual genotypes. Drought-tolerant genotypes maintained or increased AMF relative abundance, diversity, and functional integrity under drought, whereas susceptible genotypes displayed opposing changes in the community's structure. Although most genotypes displayed high dissimilarity in AMF community structure between control and drought conditions, tolerant genotypes reorganized their communities through increase in the relative abundance of key ASVs, whereas susceptible genotypes experienced substantial reductions in abundance, diversity, and specialist ASVs. Niche occupancy and functional guild analyses further showed that AMF communities in tolerant genotypes were dominated by specialist and symbiotrophic ASVs, whereas susceptible genotypes shifted toward rare and functionally reduced assemblages. At the plant level, AMF community stability was positively associated with root biomass and negatively associated with foliar nutrient, indicating a tight coupling between mycorrhizal community structure, host nutritional status, and growth. Collectively, our findings indicate that drought tolerance in common bean emerges, at least in part, from a cooperative host-microbiome strategy in which the host actively regulates the structure and functional stability of AMF communities under water stress. These results advance our understanding of plant-mycorrhizal interactions in drought adaptation and highlight the potential of integrating mycorrhizal functionality into plant breeding strategies aimed at developing climate-resilient crops.},
}

@article {pmid42147430,
year = {2026},
author = {Liu, D and Chen, Y and Pan, J and He, Z and Zhou, Y and Dai, G and Dai, X and Lin, Z and Zhao, P and Lu, H and Zheng, M},
title = {Effect of modified Zengye decoction on age-related constipation via modulation of the host-microbial metabolic axis.},
journal = {Gastroenterology report},
volume = {14},
number = {},
pages = {goag031},
pmid = {42147430},
issn = {2052-0034},
abstract = {BACKGROUND: Constipation is a common digestive disorder in the elderly caused by weakened intestinal peristalsis and reduced mucus secretion that significantly impacts quality of life. Current treatments typically provide only temporary symptomatic relief and may lead to dependence and adverse effects.

METHODS: This study investigated the therapeutic effects of a modified traditional Chinese formula, modified Zengye decoction (MZD) on age-related constipation by modulating the gut microbiome and metabolomics. Aged constipated rats were gavage-fed with or without MZD. After detection of the indicators related to the disease, the microbial and metabolic profiles were generated for all the fecal samples by using 16S rRNA gene sequencing and [1]H nuclear magnetic resonance ([1]H NMR) spectroscopy, respectively.

RESULTS: MZD effectively alleviated constipation symptoms in aged mice by enhancing the intestinal peristalsis and antioxidant capacity. Gut microbiome analysis revealed that MZD significantly altered the abundance of Firmicutes, Bacteroidetes, and Actinobacteria. Specifically, the abundance of beneficial bacteria such as Corynebacterium, Roseburia, and Clostridium increased by 6-fold, 4-fold, and 3-fold, respectively. These changes in microbial composition enhanced the production of short-chain fatty acids (SCFAs), including acetate, propionate, and butyrate. Additionally, MZD significantly increased the expression of Mucin 2 protein and the moisture content of the small intestine, while decreasing pro-inflammatory cytokines such as tumor necrosis factor-alpha, interleukin-1 beta, and interleukin-6, and increasing anti-inflammatory interleukin-10, which may be attributed to the elevated levels of SCFAs.

CONCLUSIONS: By effectively regulating the gut microbiome and SCFA metabolism, MZD demonstrated significant anti-inflammatory and mucus-secretion-promoting effects, showing therapeutic potential for age-related constipation, enteritis, and other inflammation-related intestinal diseases.},
}

@article {pmid42147745,
year = {2026},
author = {Li, W and Jiang, J and Zhou, J and Li, P and Duan, X},
title = {Gut Microbiota Metabolite, Trimethylamine N-Oxide, Aggravates Cognitive Impairment in Cerebral Ischemia-Reperfusion Injury.},
journal = {International journal of general medicine},
volume = {19},
number = {},
pages = {594053},
pmid = {42147745},
issn = {1178-7074},
abstract = {PURPOSE: Cerebral ischemia-reperfusion injury (CIRI) causes neuronal inflammation, oxidative stress, and cognitive impairment. We hypothesized that gut microbiota dysbiosis exacerbates post-ischemic cognitive deficits, with trimethylamine N-oxide (TMAO) acting as a potential mediator.

METHODS: In the primary experiment, mice received an antibiotic cocktail for 28 days to induce gut dysbiosis prior to bilateral common carotid artery occlusion (BCCAO), a model of CIRI (n = 12 per group). Gut microbial composition was analyzed using 16S rRNA sequencing, and cognitive function was assessed with the Morris water maze. Functional enrichment analyses (Kyoto Encyclopedia of Genes and Genomes and Clusters of Orthologous Groups) and microbiota-metabolite database mapping were used to identify candidate metabolites. In a separate validation cohort (n = 6 per group), TMAO (6.5 mg/day) was administered intraperitoneally for 7 days before BCCAO.

RESULTS: Antibiotic treatment markedly altered microbial diversity and composition, characterized by an expansion of Proteobacteria and a reduction in Lactobacillus. Bioinformatic analyses identified TMAO, a metabolite associated with Proteobacteria/Enterobacteria, as a potential mediator. Mice with antibiotic-induced dysbiosis subjected to CIRI exhibited impaired spatial memory, as indicated by fewer platform crossings and reduced time spent in the target quadrant. Similarly, TMAO pretreatment reproduced these cognitive deficits in BCCAO mice.

CONCLUSION: Antibiotic-induced gut dysbiosis appears to exacerbate CIRI-related cognitive impairment, at least in part through elevated TMAO levels. These findings highlight a potential microbiota-metabolite axis as a target for therapeutic intervention.},
}

@article {pmid42147973,
year = {2026},
author = {Wardi, M and Amin, AB and El Belghiti, I and Lemkhente, Z and Belmouden, A},
title = {Importance of human microbiome: an update.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1787662},
pmid = {42147973},
issn = {2813-4338},
abstract = {Millions of microorganisms-including bacteria, viruses, fungi, archaea, and protists-reside on and within the human body, collectively forming the human microbiota. This complex and dynamic community plays a crucial role in modulating physiological processes, particularly the development and regulation of the immune system. Modern behaviors such as frequent washing, excessive hygiene, and widespread use of antimicrobial agents can disrupt the natural composition and functional balance of the microbiota, leading to altered immune responses and increased susceptibility to disease. In this review, we focus primarily on the bacterial component of the human microbiome. While we acknowledge the importance of viruses, fungi, archaea, and protists, these components are beyond the scope of the current review. We highlight recent advances in bacterial microbiome research that are reshaping our understanding of host-microbe interactions, immune modulation, and the health consequences of microbiota dysbiosis.},
}

@article {pmid42148043,
year = {2026},
author = {Huang, CY and Nuwagira, E and Tisza, M and Kim, M and Tayebwa, M and Vieira, J and Lam, N and Wallach, E and Wiens, M and Tsai, AC and Valeri, L and Vallarino, J and Allen, JG and Lai, PS},
title = {Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.},
journal = {Environmental health perspectives},
volume = {134},
number = {1},
pages = {75-90},
doi = {10.1021/EHP.6c00064},
pmid = {42148043},
issn = {1552-9924},
mesh = {Humans ; Uganda ; Female ; *Gastrointestinal Microbiome ; *Air Pollution, Indoor/statistics & numerical data/adverse effects ; Adult ; *Virome ; Middle Aged ; },
abstract = {BACKGROUND: Emerging observational studies suggest that air pollution can influence the gut microbiome. However, this association is often highly confounded by factors, such as diet and poverty. The gut virome may influence respiratory health independent of the gut microbiome. We recently demonstrated in a randomized waitlist-controlled trial (ClinicalTrials.gov NCT03351504) that a clean lighting intervention reduced the level of personal exposure to air pollution among adult women in rural Uganda. OBJECTIVES: To determine the effect of a solar lighting intervention on changes to the gut microbiome and virome and secondarily to determine the association between these changes on lung health. METHODS: Between 2018 and 2019, we collected stool samples and assessed respiratory symptoms and spirometry from 80 adult women living in rural Uganda at baseline and 12 and 18 months postrandomization. The intervention group received a solar lighting system after randomization, while the waitlist-controlled group received one at 12 months. Deep metagenomics sequencing of stool was performed and profiled for nonviral and viral taxonomic composition. The primary analysis focused on pre- vs postintervention changes due to power considerations, adjusting for potential confounding by age, diet, antibiotic use, and season. A sensitivity analysis was conducted using intention-to-treat principles. When comparing pre- vs postintervention periods, we used sparse partial least-squares models to identify nonviral and viral signatures of reduced air pollution exposure. Mixed effects models were used to evaluate changes in health outcomes as well as associations between microbial signatures of reduced air pollution exposure and health. RESULTS: The average age was 39.2 years. The solar lighting intervention led to larger changes in viral compared to nonviral microbial community structure and differential abundance of bacteria, eukaryotes, and viruses. Provision of solar lighting systems was associated with a reduction in the presence of respiratory symptoms from 57.1% to 36.1% (p = 0.002), while there was no impact on lung function. Microbiome and virome signatures had AUCs of 0.74 and 0.76, respectively, in predicting pre- vs postintervention stool samples. Microbiome signatures were associated with a lower risk of respiratory symptoms (OR = 0.68 (0.49 - 0.94), p = 0.020). CONCLUSION: Among adult women living in rural Uganda, both nonviral and viral components of the gut microbial community changed after a clean lighting intervention. Microbiome signatures reflective of lower air pollution exposures were associated with improved respiratory symptoms. These observations suggest that air pollution may influence lung health through the gut-lung axis, warranting further exploration in future intervention studies.},
}

Humans
Uganda
Female
*Gastrointestinal Microbiome
*Air Pollution, Indoor/statistics & numerical data/adverse effects
Adult
*Virome
Middle Aged

@article {pmid42148231,
year = {2026},
author = {Niu, Y and Li, Y and Zhou, X and Kong, W and Zhou, B and Hu, X and Guo, J},
title = {Geraniol alleviates benzo[a]pyrene-induced neurotoxicity by regulating the NLRP3/Caspase-1 pathway and gut microbiome in mice.},
journal = {Food science and biotechnology},
volume = {35},
number = {7},
pages = {1905-1918},
pmid = {42148231},
issn = {2092-6456},
abstract = {Benzo[a]pyrene (BaP) exposure has been associated with an increased risk of neurotoxicity, including learning and memory impairment. As an antioxidant and a potential prebiotic, geraniol is speculated the potential preventive agent against neurotoxicity. This study aims to reveal the neuroprotection of geraniol on BaP-induced neurotoxicity. The results indicate geraniol increases immunofluorescence intensity of PSD-95, and decreases the immunofluorescence intensity of Iba-1 and GFAP, as well as the level of inflammatory cytokines, and pyroptosis biomarkers. Geraniol also up-regulates the expression of tight junction proteins markedly. In addition, lipopolysaccharide (LPS), might originate from intestinal flora and closely correlated with inflammation and pyroptosis, varies in brain and serum between each group. It is summarized that the underlying mechanism of neuroprotection effect of geraniol might be located on improving intestinal physical barrier function, decreasing LPS releasing, down-regulating pyroptosis and inflammatory response, thereby alleviating neurotoxicity induced by BaP in mice model.},
}

@article {pmid42148333,
year = {2026},
author = {Szalus, K and Sakowicz-Burkiewicz, M and Pawełczyk, T and Nowicki, RJ and Trzeciak, M},
title = {The mRNA levels of COL1A1, COL2A1, COL3A1 and COL4A1 in non-lesional and lesional skin of atopic dermatitis patients.},
journal = {Postepy dermatologii i alergologii},
volume = {43},
number = {1},
pages = {94-100},
pmid = {42148333},
issn = {1642-395X},
abstract = {INTRODUCTION: Atopic dermatitis (AD) is a complex, multifactorial inflammatory disease. The multifaceted aetiology and pathophysiology consist of different elements, including genetic and immunological disorders, skin barrier defects, microbiome dysbiosis and environmental interactions. To date, little has been known about the genes involved in the relationship between extracellular matrix (ECM) expression and the pathogenesis of atopic dermatitis.

AIM: The aim of our study was to examine the mRNA transcript levels of genes encoding collagen type I, II, III and IV in the skin of atopic dermatitis patients vs. controls and to search for associations with subjective clinical symptoms and disease severity.

MATERIAL AND METHODS: A total of 18 subjects participated in the study. Nine biopsies were taken from lesions, nine from non-lesional AD skin and nine from healthy volunteers. The mRNA levels of COL1A1, COL2A1, COL3A1 and COL4A1 were determined using real-time RT-PCR. AD severity was evaluated by calculating the SCORAD score and measuring the pruritus intensity using the Visual Analogue Scale (VAS).

RESULTS: A significant increase in the mRNA levels of COL3A1 in the study group compared to the control group was associated with an increase in the intensity of clinically reported symptoms as assessed by the SCORAD and the itching scale VAS (p = 0.0293). In addition, there was a statistically significant difference in the mRNA levels of the COL3A1 gene and the mRNA levels of the COL4A1 gene between subjects in the lesional and non-lesional skin of the study group. The transcript level of mRNA COL3A1 was statistically higher in lesional skin than in non-lesional skin among subjects with AD than in healthy volunteers. Conversely, mRNA COL4A1 expression was significantly higher in non-lesional skin than in lesional skin among AD subjects; however, there was no statistical difference between AD subjects and healthy volunteers.

CONCLUSIONS: Our results suggest a role for collagen mRNA levels in AD pathogenesis. Further studies are needed to assess its role as a new potential biomarker, as a predictive element for assessing the intensity of AD or as a new target for AD therapy in the era of personalized medicine. The question to be answered is the importance of remodelling processes in AD.},
}

@article {pmid42148336,
year = {2026},
author = {Kalicka, M and Biadasiewicz, M and Tekielak, A and Frątczak, A and Bergler-Czop, B},
title = {The role of the skin microbiome in modulating rosacea.},
journal = {Postepy dermatologii i alergologii},
volume = {43},
number = {1},
pages = {1-6},
pmid = {42148336},
issn = {1642-395X},
abstract = {INTRODUCTION: The skin microbiome is a contributing factor in the pathogenesis of rosacea, and disturbances in its composition may play a pivotal role in the development of the disease.

METHODS: A review of the literature in PubMed and Embase databases from inception to February 2025 to identify 13 scientific studies on the influence of the skin microbiome on the modulation of the course of rosacea.

RESULTS: Rosacea patients consistently exhibit microbial dysbiosis, which is characterized by an increased bacterial diversity, particularly involving pro-inflammatory taxa such as Staphylococcus epidermidis, Corynebacterium, and Streptococcus.

CONCLUSIONS: It seems there is growing evidence to suggest a link between the skin microbiome and the development of rosacea. This link involves changes in bacterial composition, interactions with the immune system, and the induction of inflammation. However, therapeutic implications remain largely speculative.},
}

@article {pmid42148465,
year = {2026},
author = {Chang, J and Bhuvanagiri, GM and Dulkanchainun, M and Wang, C},
title = {Osteoporosis and Periodontitis: Two-Way Epidemiological and Mechanistic Evidence.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70125},
pmid = {42148465},
issn = {1600-0765},
support = {R01 DE029200/DE/NIDCR NIH HHS/United States ; },
abstract = {Osteoporosis and periodontitis are highly prevalent, chronic inflammatory diseases that constitute a major global health burden. Strong epidemiological evidence shows an association between the two diseases, in which osteoporosis patients have an increased risk of periodontitis, specifically in postmenopausal women. Osteoporosis and periodontitis are linked by bidirectional relationships through shared inflammatory and bone-resorptive pathways. Such a connection is explained by shared osteo-immunologic pathways, particularly as highlighted by recent breakthrough findings in the field. In this review, we comprehensively examined the seven links between osteoporosis and periodontitis across microbial translocation, systemic meta-inflammation, maladaptive myelopoiesis, immune cell trafficking, masticatory dysfunction-diet interactions, underlying vulnerabilities, and functional alterations of the oral microbiome, drawing on current biological findings and clinical evidence. This bidirectional relationship underscores the importance of integrated medical and dental screening and management strategies to improve patient outcomes for both conditions.},
}

@article {pmid42148573,
year = {2026},
author = {Raad, R and Mann, A and Pal, A and Parra, A and Strawn, L and Hamilton, A and Critzer, F and den Bakker, HC},
title = {Metagenomic profiling of bacterial (16S) and fungal (ITS) communities on d'Anjou pears during long-term controlled-atmosphere storage.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0411725},
doi = {10.1128/spectrum.04117-25},
pmid = {42148573},
issn = {2165-0497},
abstract = {D'Anjou pears are routinely stored for up to nine months under controlled-atmosphere (CA) conditions to meet market demands. While this practice maintains fruit quality, limited information exists on pears' natural microbiota throughout storage. The objective of this study was to describe fungal and bacterial composition on marketable and unmarketable conventional, whole, intact pears under two storage practices (bulk vs wrapped) at 3, 6, and 9 months in long-term CA cold storage. Storage practices had a significant effect on the composition and succession of both fungal and bacterial communities. No significant differences in Chao1 index were found between the bacterial and fungal communities on marketable or unmarketable pears. Trends in Chao1 indices of fungal and bacterial communities peaked at mid-storage and declined by 9 months, with wrapped pears showing parallel trends, and bulk pears exhibiting a sharper late-stage reduction. No distinct clusters could be found for 3- and 6-month fungal communities, irrespective of marketability, or whether bulk or wrapped. The principal coordinate analysis of the bacterial communities showed tight clustering by time point for the individually wrapped pears, irrespective of their marketability. Bacterial communities included genera common in food-processing and plant environments, such as Pseudomonas (19.2% relative abundance [RA]) and Acinetobacter (3.31% RA). Fungal communities shifted over time, with spoilage-associated genera like Aureobasidium (23.3% RA), Penicillium (9.28% RA), Botrytis (0.33% RA), and Mucor (0.14% RA) present at different storage stages.IMPORTANCEThis study highlights the influence of storage duration and packaging on microbial succession, establishing initial benchmarks of pear surface microbiomes. The observed lack of significant differences in microbial diversity between marketable and unmarketable pears suggests that these baseline community profiles can serve as critical reference points for identifying other influential factors. Variables such as handling practices may exert a more direct effect on microbial dynamics and, consequently, product quality. Establishing these baselines is essential because they provide a foundation for detecting deviations linked to spoilage or safety risks. Moreover, understanding these patterns can guide the development of targeted microbial control strategies in postharvest systems, enabling interventions that maintain fruit quality, reduce losses, and possibly improve food safety throughout the supply chain.},
}

@article {pmid42148579,
year = {2026},
author = {Liu, M and Zhang, W and Zhang, J and Lv, N and Wu, X and Alalawy, AI and Zhao, W and Bao, H and Wu, J},
title = {Multi-site microbiomes' response to chronic obstructive pulmonary disease.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0000726},
doi = {10.1128/spectrum.00007-26},
pmid = {42148579},
issn = {2165-0497},
abstract = {This study aimed to evaluate changes in the oral, nasal, pulmonary, and gut microbiota in patients with chronic obstructive pulmonary disease (COPD) and to explore their interrelationships compared with the healthy group. This study included 33 COPD patients and 29 healthy individuals. A total of 162 oral, nasal, sputum, and fecal samples were obtained. The microbiota was determined using full-length 16S rRNA gene sequencing on the PacBio platform. Alpha diversity was significantly reduced in sputum and fecal samples of COPD patients, while oral and nasal microbiota showed no significant differences. Beta diversity revealed substantial overlap between oral and sputum microbiota in both groups, while nasal and fecal communities were clearly distinct. Linear discriminant analysis effect size analysis identified Haemophilus parahaemolyticus as a sputum biomarker. Source tracking confirmed that the majority of lung microbiota originated from the oral cavity. Interleukin-6 was inversely correlated with short-chain fatty acids (SCFAs)-producing microbiota in fecal samples, suggesting that depletion of these bacteria may contribute to systemic inflammation. Co-occurrence network analysis revealed that the sputum microbial network in COPD patients exhibited reduced robustness and lacked prominent hub nodes. Lung microbiota largely originates from the oral cavity but is changed in COPD. The lung microbiome is still more sensitive and accurate than the oral, nasal, and fecal microbiomes for COPD diagnosis. Fragmented networks in COPD indicate reduced community resilience.IMPORTANCELung and gut microbial diversity is significantly reduced in COPD patients. Oral microbiota is the primary source of lung microbes, but poorly predicts COPD status. Haemophilus parahaemolyticus was identified as a novel sputum biomarker in COPD. The bacterial network in COPD lungs is fragmented, lacking the resilience seen in healthy individuals.},
}

@article {pmid42148581,
year = {2026},
author = {Wang, K and Zhang, D and Shen, K and Qiu, Y and Deng, B and Zhou, J and Qiu, S},
title = {Multi-omics characterization of new and aged Daqu reveals region-specific microbial succession and metabolic signatures in Maotai-flavor liquor fermentation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0377525},
doi = {10.1128/spectrum.03775-25},
pmid = {42148581},
issn = {2165-0497},
abstract = {Daqu is an essential fermentation starter that drives the formation of the characteristic flavor of Maotai-flavor liquor, yet the ecological and metabolic mechanisms underlying its regional differentiation and maturation remain poorly resolved. Here, we performed genome-resolved metagenomic and untargeted metabolomic analyses on 48 new and aged Daqu samples collected from four major Maotai-flavor liquor-producing regions in Guizhou Province, China. We reconstructed 163 high-quality metagenome-assembled genomes (MAGs) spanning 16 bacterial and 3 archaeal phyla and identified 2,642 metabolites across ionization modes. Distinct regional microbial signatures were observed, with Jinsha Daqu showing the greatest genomic diversity and unique MAGs, whereas Maotai Daqu exhibited the highest community similarity with other regions. Aged Daqu significantly increased microbial richness and functional capacity, enriching thermophilic and spore-forming taxa (e.g., Bacillus, Lentibacillus, Kroppenstedtia) and enhancing carbohydrate-active enzymes (GH13, GH43, and GH3), amino acid degradation, lipid metabolism, and secondary metabolic pathways. Metabolomic profiling revealed elevated amino acid derivatives, fatty acids, esters, and phenolic compounds in aged Daqu, indicating intensified biochemical activity. Multi-omics integration linked dominant microorganisms-including Bacillus thuringiensis, Actinomycetaceae bacterium, and Methylocaldum szegediense to pyrazine biosynthesis, amino acid catabolism, and lipid oxidation, forming coordinated microbial-metabolite modules that underlie region-specific flavor precursor formation. These findings establish a mechanistic model in which microbial terroir, aging-driven succession, and metabolic specialization jointly shape the maturation and flavor potential of Maotai-flavor liquor.IMPORTANCEThis study provides the first genome-resolved, multi-omics framework for understanding how geographic origin and storage aging co-regulate the ecological assembly, functional specialization, and metabolic transformation of Maotai-flavor liquor. By linking specific MAGs, functional pathways, and key flavor precursors, our results offer mechanistic insights into microbial terroir and provide a scientific foundation for microbiome-guided optimization of Maotai-flavor liquor quality.},
}

@article {pmid42136740,
year = {2026},
author = {Chen, Y and Li, J and Sun, Y and Yue, X and Tian, XH and Liu, F and Wang, DY and Shen, J},
title = {Biofilm-targeted liposomal curcumin delivery system for anti-caries therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1808450},
pmid = {42136740},
issn = {2235-2988},
mesh = {*Biofilms/drug effects ; *Liposomes/chemistry ; *Dental Caries/drug therapy/microbiology ; Animals ; *Curcumin/administration & dosage/pharmacology ; Streptococcus mutans/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Drug Delivery Systems ; Rats ; Hydrogen-Ion Concentration ; Humans ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Dental caries, driven by acidogenic biofilms, remains a major global health challenge. Current chemical treatments, such as chlorhexidine and fluoride, can disrupt oral microbial homeostasis and cause adverse effects, including tooth discoloration, dentin hypersensitivity, and taste disturbances. Curcumin, a natural photosensitizer, exhibits antibacterial activity and favorable biocompatibility, however, its clinical application is limited by poor stability, low aqueous solubility, and restricted biofilm penetration. There is an urgent need to develop innovative therapeutic strategies to enhance curcumin transport into acidic cariogenic biofilms.

METHODS: We developed a pH-responsive liposomal delivery system (Cur/DCPA-H2O) engineered to penetrate acidic cariogenic biofilms and enhance curcumin transport. The physicochemical characterization of Cur/DCPA-H2O was performed using a UV-1800 spectrophotometer, transmission electron microscopy (TEM), and dynamic light scattering (DLS). Biocompatibility was assessed by Cell Counting Kit-8 (CCK-8) assays, hemolysis tests, and Live/Dead cell staining. The antibacterial efficacy in vitro and ex vivo was evaluated using colony-forming unit (CFU) counting, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and crystal violet (CV) staining. An in vivo caries model was established to assess the therapeutic efficacy of Cur/DCPA-H2O, using micro-computed tomography (micro-CT), Keyes' scoring, and 16S rRNA sequencing.

RESULTS: The liposomes exploit charge reversal to interact with representative caries-associated bacteria (Streptococcus mutans and the early colonizer Streptococcus sanguinis), enabling deep biofilm penetration. Upon light irradiation, Cur/DCPA-H2O was observed to generate reactive oxygen species (ROS), which may contribute to partial disruption of the biofilm matrix and reduced bacterial viability in vitro. In a rat caries model, treatment with Cur/DCPA-H2O under light irradiation reduced caries severity and decreased lesion depth by approximately 50%. It also shifted the oral microbiome composition toward a less dysbiotic profile, as confirmed by 16S rRNA sequencing.

DISCUSSION: This study demonstrates that a biofilm-targeted, pH responsive liposomal curcumin delivery system may provide a safe and effective strategy for caries prevention, highlighting the potential of natural therapeutics to modulate pathogenic biofilms with limited impact on the overall microbial community.},
}

*Biofilms/drug effects
*Liposomes/chemistry
*Dental Caries/drug therapy/microbiology
Animals
*Curcumin/administration & dosage/pharmacology
Streptococcus mutans/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Drug Delivery Systems
Rats
Hydrogen-Ion Concentration
Humans
Disease Models, Animal

@article {pmid42136780,
year = {2026},
author = {Ahmed, SH and Islam, ZS and Zaidi, SM and Khalid, T},
title = {Surgical Solution of C-Section Associated Surgical Site Infection in LMICs: A Narrative Review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {411AASC},
pages = {S122-S129},
pmid = {42136780},
issn = {1682-024X},
abstract = {Cesarean section (CS) is a life-saving procedure worldwide, accompanied by a substantial burden of surgical site infections (SSIs), with the most significant impact felt in low- and middle-income countries (LMICs). This review consolidates current knowledge on the surgical management of post-cesarean infections, highlighting the vaginal microbiome as a key source of infection and the physiological immunosuppression in the postpartum period. We describe the categories of deep and organ-space SSIs that require operative management, from wound debridement to laparoscopic drainage and laparotomy. The analysis also assesses proven preventive measures, such as dual-agent antibiotic prophylaxis, advanced closure techniques, and structured care bundles. It includes a standardized, context-sensitive checklist designed for LMICs, which combines pre, intra, and postoperative measures to prevent and manage SSIs, with the aim to reduce maternal morbidity and mortality in resource-limited settings.},
}

@article {pmid42136862,
year = {2026},
author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M},
title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1805596},
pmid = {42136862},
issn = {2296-858X},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.

OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.

METHODS: Skin samples were collected from 12 AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).

RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p = 0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p = 0.042) and between moderate and severe groups (p = 0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.

CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.},
}

@article {pmid42136892,
year = {2026},
author = {Hu, CY and Pai, AH and Wang, YW and Lu, PC and Wu, HM and Huang, HY},
title = {Endobiota-Estrobolome Profiles in Reproductive-Aged Women With Ovarian Endometriosis.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70061},
pmid = {42136892},
issn = {1445-5781},
abstract = {PURPOSE: This case-control study investigated whether ovarian endometriosis is associated with altered estrogen metabolism and gut or urogenital microbiota by analyzing enzyme activity, bacterial composition, and variations of estrogen metabolites in fecal, vaginal, and urinary samples.

METHODS: Thirty-eight reproductive-aged women were enrolled, including 24 with pathologically confirmed ovarian endometriosis and 14 controls. Stool, urine, and vaginal samples were collected preoperatively. Gut β-glucuronidase and β-glucosidase activities were measured, estrogen and 14 metabolites were quantified using liquid chromatography-mass spectrometry, and gut and vaginal microbiota were analyzed by 16S rRNA gene sequencing. Microbial composition, diversity, and abundance were compared between groups.

RESULTS: Gut β-glucuronidase activity and overall microbial diversity were comparable between groups; however, the control group showed a higher prevalence of the genus Rothia, whereas several genera, including Megamonas and [Eubacterium] coprostanoligenes_group, were enriched in the ovarian endometriosis group. In contrast, vaginal samples from patients with ovarian endometriosis demonstrated significantly reduced bacterial abundance and diversity, accompanied by lower levels of 4-methoxyestrone, 2-methoxyestrone, and 2-hydroxyestrone-3-methyl ether.

CONCLUSIONS: Although overt dysbiosis was not observed, specific microbial shifts and altered estrogen metabolites may reflect disturbances in estrogen metabolism and urogenital-gastrointestinal microbiota in ovarian endometriosis.},
}

@article {pmid42136931,
year = {2026},
author = {Mweetwa, MN and Ahsan, K and Louis-Auguste, J and Besa, E and Posma, JM and McNulty, NP and Barratt, MJ and Gordon, JI and Kelly, P},
title = {Erratum: Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial - CORRIGENDUM.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e6},
doi = {10.1017/gmb.2026.10025},
pmid = {42136931},
issn = {2632-2897},
abstract = {[This corrects the article DOI: 10.1017/gmb.2025.10011.].},
}

@article {pmid42137127,
year = {2025},
author = {Ahmadi, N and Hossein Tehrani, MJ and Alamdary, A and Moukhah, R and Mardani, R and Shahali, M},
title = {Gut microbiome dysbiosis and inflammatory markers in severe COVID-19: links to atherosclerosis and potential therapeutic insights.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {110-120},
pmid = {42137127},
issn = {2008-2258},
abstract = {BACKGROUND: COVID-19 is implicated in the exacerbation of atherosclerosis, potentially leading to its clinical manifestations. The aim of this study was to evaluate serum biomarkers, including albumin (ALB), C-reactive protein (CRP), ferritin (FERR), CD16, CD18, NLRP3, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), in patients with COVID-19. In addition, assessment of microbiome profiles may provide insights into disease severity and gastrointestinal health.

METHOD: In this case-control study, serum samples were collected from 90 individuals: 30 patients with COVID-19 admitted to the intensive care unit, 30 hospitalized patients with COVID-19, and 30 healthy individuals. Concentrations of ALB, CRP, FERR, NLRP3, CD16, CD18, IL-6, and TNF-α were measured. Quantitative PCR (qPCR) was used to assess microbial diversity in stool samples.

RESULT: No significant age difference was noted between the patient (55.40 ± 10.34 years) and the control groups (58.34 ± 11.71 years). Substantial increases in CRP, CD-18, CD-16, IL-6, Alb, and TNF-α (P < 0.001) were observed in severe cases compared to non-severe cases. Microbiome analysis indicated a 40% decrease in Roseburia and a 35% reduction in Faecalibacterium in ICU patients.

CONCLUSION: Evaluating these biomarkers provides critical insights into atherosclerosis susceptibility in COVID-19 patients and reveals meaningful relationships among COVID-19, atherosclerosis, and gastrointestinal health.},
}

@article {pmid42137129,
year = {2025},
author = {Tavanaeian, S and Feizabadi, MM and Falsafi, S and Asadzadeh Aghdaei, H},
title = {Machine learning and microbiome analysis for early detection of pancreatic cancer.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {76-84},
pmid = {42137129},
issn = {2008-2258},
abstract = {AIM: To develop machine learning (ML) models integrating clinical and microbial predictors for early pancreatic cancer (PC) detection.

BACKGROUND: Pancreatic cancer is a leading cause of cancer-related mortality, with a 5-year survival rate of ~12%. Limited biomarkers and non-specific risk factors hinder early diagnosis. Emerging evidence links oral and gut microbiota, such as Fusobacterium nucleatum and Roseburia species, to PC risk, offering potential for non-invasive biomarkers.

METHODS: We analyzed a retrospective cohort of 40 participants (20 PC cases, 20 controls). Clinical (e.g., age, WBC) and microbial (e.g., Fusobacterium nucleatum, Roseburia-to-Fusobacterium ratio [RI/FN]) predictors were evaluated using five ML classifiers (logistic regression, SVM, random forest, naïve Bayes, neural network) under Leave-Group-Out Cross-Validation (LGOCV; 80/20 split, 200 repetitions). Elastic-net regularization and stability selection identified key predictors. Performance metrics included AUC, sensitivity, specificity, PPV, NPV, and accuracy. Nomograms were developed for clinical utility.

RESULTS: Age (AUC 97.4%) and microbial markers (e.g., RI/FN ratio, AUC 100%) showed excellent discrimination. Multivariable models using age and RI/FN achieved excellent performance (AUC 98-100%). Nomograms provided interpretable risk estimates.

CONCLUSIONS: Integrating clinical and microbial predictors with ML offers a promising approach for non-invasive PC detection. The RI/FN ratio and age are robust biomarkers that warrant further validation in larger cohorts. However, the small sample size limits generalizability and warrants validation in larger cohorts.},
}

@article {pmid42137133,
year = {2025},
author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K},
title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {85-96},
pmid = {42137133},
issn = {2008-2258},
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).

METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.

RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.

CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.},
}

@article {pmid42137389,
year = {2026},
author = {El Halabi, L and AlBayeh, A and Khoury, A and Katrib, M and Nasr, J and Al-Obaidi, A},
title = {Vitamins and Cancer Risk: A Comprehensive Review of Epidemiologic and Clinical Evidence.},
journal = {Kansas journal of medicine},
volume = {19},
number = {Suppl 1},
pages = {12},
doi = {10.17161/kjm.vol19.25377},
pmid = {42137389},
issn = {1948-2035},
abstract = {INTRODUCTION: Vitamin supplementation nearly is universal among patients with cancer, yet the scientific landscape is far more complex. Across decades of research, vitamins have demonstrated profound biological effects ranging from immune activation and ferroptosis modulation to paradoxical tumor promotion.

OBJECTIVE: This scoping review maps the breadth of compelling and controversial evidence surrounding vitamins A, D, E, K, C, and the B-complex in cancer prevention, treatment response, and toxicity.

METHODS: Guided by PRISMA-ScR domains, we synthesized mechanistic studies, epidemiologic cohorts, randomized trials, and therapeutic investigations addressing vitamins in the oncology context. Eligibility focused on sources examining cancer risk, progression, treatment interactions, or toxicity.

RESULTS: Several vitamins exhibit striking anticancer mechanisms: vitamin K2 triggers autophagy-driven leukemia cell death; pharmacologic vitamin C selectively kills KRAS- and BRAF-mutated colorectal cancer cells; niacin reshapes the tumor immune microenvironment; and vitamin D enhances microbiome-dependent antitumor immunity. Yet the review also identifies potential harms, including beta-carotene increasing lung cancer risk in smokers, vitamin E raising prostate cancer risk, and antioxidant supplementation potentially weakening the oxidative mechanisms essential for chemotherapy and radiotherapy efficacy. Dose-response patterns frequently are U-shaped, with both deficiency and excess linked to greater risk. High-dose intravenous vitamin C, vitamin D repletion during immunotherapy, and vitamin-targeted nanoparticles emerge as promising but unproven therapeutic strategies.

CONCLUSIONS: Across vitamins, benefits appear highly context-dependent. Routine supplementation is unsupported, while targeted correction of true deficiencies remains essential. This rapidly evolving field demands individualized decision-making and rigorously designed trials to define when vitamins act as allies, and when they become adversaries, in cancer care.},
}

@article {pmid42137425,
year = {2026},
author = {Miki, T and Ito, M and Haneda, T and Okada, N and Kim, YG},
title = {Infection strategies of SalmonellaTyphimurium for gut-lumen colonization: Overcoming host defenses, exploiting host responses, and adapting to the enteric niche.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2671472},
pmid = {42137425},
issn = {2993-3935},
abstract = {Diarrheal disease is a leading cause of child morbidity and mortality globally, largely resulting from contaminated food and water and exposure to enteric pathogens. Salmonella enterica serovar Typhimurium (STm) is an enteropathogenic bacterium that infects the gastrointestinal tract using diverse strategies that are still being elucidated. Meanwhile, the gut comprises a complex ecosystem known as the microbiome, which is densely inhabited by microbial communities. The microbiome confers colonization resistance against enteropathogenic bacteria, whereas STm can overcome these defenses to establish infection. Here, we review STm infection strategies in the gut, with a particular focus on evidence from mouse models. Understanding STm virulence mechanism and adaptation strategies may inform the development of targeted interventions to prevent and treat gastrointestinal infection.},
}

@article {pmid42137495,
year = {2026},
author = {Sekito, T and Hirakawa, H and Sadahira, T},
title = {Unraveling the vaginal microbiota-based etiology of recurrent cystitis: the potential role of Lactobacillus vaginal suppositories.},
journal = {Therapeutic advances in urology},
volume = {18},
number = {},
pages = {17562872261448600},
pmid = {42137495},
issn = {1756-2872},
abstract = {Recurrent cystitis is a common problem in women that substantially impairs quality of life and contributes to increasing healthcare costs. Traditionally regarded as an ascending infection originating from the gut, recurrent cystitis is now increasingly understood as a disorder rooted in vaginal dysbiosis, with the vagina acting as a key reservoir for uropathogenic Escherichia coli. Loss of a Lactobacillus-dominant vaginal microbiota and overgrowth of enteric and anaerobic bacteria are strongly associated with recurrent cystitis, particularly in postmenopausal women. Lactobacillus species promote vaginal health by producing lactic acid, maintaining a low pH, generating antimicrobial compounds, inhibiting pathogen adhesion, and modulating mucosal immune responses. At the same time, long-term antimicrobial prophylaxis, although effective in reducing recurrences, is limited by adverse effects and the promotion of antimicrobial resistance. These concerns have driven interest in strategies that restore the protective vaginal ecosystem rather than relying on repeated antimicrobial exposure. This narrative review summarizes current concepts linking vaginal dysbiosis to recurrent cystitis, highlights the protective role of Lactobacillus, and synthesizes clinical data on Lactobacillus vaginal suppositories, particularly Lactobacillus crispatus (L. crispatus)-based preparations, as a targeted, non-antimicrobial prophylactic option. Across pilot, phase II, and randomized trials, Lactobacillus vaginal therapy has demonstrated a generally favorable safety and tolerability profile, with preliminary evidence suggesting a potential to reduce recurrent cystitis episodes while restoring a Lactobacillus-dominant vaginal microbiota. However, larger, standardized studies are still needed. Collectively, these findings provide a rationale for investigating Lactobacillus vaginal suppositories as a microbiome-informed, non-antimicrobial strategy for the long-term prevention of recurrent cystitis, particularly in postmenopausal and other high-risk women, and highlight the importance of further research to define the role of vaginal microbiota-directed therapies in future recurrent cystitis management.},
}

@article {pmid42137543,
year = {2026},
author = {Zhang, K and Zomer, H and Potkamp, G and Salles, JF and Tieleman, BI and Dietz, MW},
title = {Seasonal Dynamics of the Gut Microbiome in Urban Feral Pigeons Are Associated With Environmental Conditions, Not With Diet Shifts.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73682},
pmid = {42137543},
issn = {2045-7758},
abstract = {Gut microbiomes play a crucial role in host physiology and seasonal adaptation. While seasonal shifts in avian gut microbiota are often attributed to seasonal diet variation, environmental factors may be equally or more important, particularly in urban ecosystems. This study aimed to determine whether seasonal variation in the gut microbiome of free-living feral pigeons (Columba livia f. domestica) inhabiting urban environments is associated with seasonal changes in diet and environmental conditions. We captured feral pigeons at three locations in Groningen, the Netherlands, during winter (January-February 2019) and summer (July-August 2019). Cloacal swabs and fecal samples were collected to assess gut microbiota via 16S rRNA sequencing and diet via DNA metabarcoding, respectively. Microbial diversity and composition showed significant seasonal variation and location effects. At Vismarkt, one of the three urban sampling sites within the city of Groningen, Firmicutes were more abundant in summer than in winter, while Actinobacteria were more abundant in winter. Dominant genera also varied seasonally, with Lactobacillus more abundant in summer. In contrast, the diet composition was dominated by Poaceae (grasses), Fabaceae (legumes), and Asteraceae (daisies) across all seasons and locations, with no detectable differences between locations or seasons. Distance-based redundancy analysis indicated that temperature was significantly associated with microbiome composition, whereas diet as measured here showed no detectable association. This suggests that seasonal microbiome variation in urban feral pigeons may be related to seasonal environmental conditions even without detectable dietary shifts, consistent with the idea that seasonal environmental conditions can contribute to microbiome seasonality in birds.},
}

@article {pmid42137790,
year = {2026},
author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D},
title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1788826},
pmid = {42137790},
issn = {1664-302X},
abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.},
}

@article {pmid42137793,
year = {2026},
author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM},
title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1641069},
pmid = {42137793},
issn = {1664-302X},
abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.},
}

@article {pmid42137801,
year = {2026},
author = {D'Amico-Willman, KM and Joglekar, P and Turner, D and Flaherty, M and Ritchie, DF and Huerta, AI},
title = {Four decades of genomic stability and adaptive divergence in Xanthomonas phages: defining Duraznoxanthovirus arenicola and its evolutionary framework.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779411},
pmid = {42137801},
issn = {1664-302X},
abstract = {Bacteriophages (phages) are abundant and ecologically significant, yet their diversity and roles in plant-associated ecosystems remain poorly understood, limiting their application in sustainable disease management. To address this gap, we characterized 15 phages infecting Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on peach, has been isolated for over four decades from North Carolina orchards. Comparative genomic and phylogenetic analyses revealed two temporally distinct clades with >95% nucleotide identity and 63 conserved core genes, forming a new genus and species, Duraznoxanthovirus arenicola. These findings challenge assumptions of pervasive genomic mosaicism, highlighting remarkable genomic stability alongside localized variability in accessory loci. Beyond genus-level characterization, our analyses support a broader taxonomic restructuring within the family Anamaviridae, introducing a new subfamily (Terravirinae) and two new genera (Duraznoxanthovirus and Ralstopathovirus). This work provides the a family-level framework for phages exclusively infecting plant-associated bacteria, offering evolutionary insights and a foundation for ecological studies and management strategies.},
}

@article {pmid42137803,
year = {2026},
author = {Liu, Y and Chen, C and Gao, J},
title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818141},
pmid = {42137803},
issn = {1664-302X},
abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.},
}

@article {pmid42137813,
year = {2026},
author = {Chiuta, NE and Pofu, KM and Mashela, PW},
title = {Short-term crop rotation interactive effects on soil microbial communities and potato yield under field conditions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807765},
pmid = {42137813},
issn = {1664-302X},
abstract = {INTRODUCTION: The inclusion of plant-parasitic nematode (Meloidogyne species) non-host crops in potato (Solanum tuberosum L.) -based cropping systems can sustainably manage the pest and reduce the application of greenhouse gas-emitting agro-chemicals. Nevertheless, there exists a research gap on how these cropping systems interact with soil microbiome.

METHODS: A 2-year field study was conducted at the University of Limpopo and the Agricultural Research Council to investigate the effects of potato monoculture, Cucumis africanus-potato, sorghum-potato and potato (Velum)-potato cropping sequences on soil health and tuber yield. The treatment crops, namely, sweet stem sorghum (Sorghum bicolor) cv. 'Ndendane-X1', C. africanus, potato cv. 'Mondial G3' and potato cv. 'Mondial G3'-velum (control), were assigned to 4 m[2] subplots in Sequence 1, in a randomized complete block design, with six replicates. The successor potato crop was planted in Sequence 2. Crop arrangement in Sequences 3 and 4 was as in Sequences 1 and 2, respectively. Soil organic carbon content, enzyme activity, nematode and bacterial functional diversity data were collected from Sequences 1 to 4. Final potato tuber yield was recorded in Sequence 4.

RESULTS: Based on the results, nematode indices revealed disturbed agroecosystems dominated with bacterial decomposition pathways, which is a common occurrence in intensively managed soils. High soil organic carbon content, microbial diversity and enzyme activity were observed in sorghum-potato and C. africanus-potato compared to potato monoculture (with or without velum), at both locations. In addition, sorghum-potato improved soil structure over time based on the nematode faunal results, thereby depicting its ability to promote soil health compared to other cropping systems. Tuber yield mass significantly varied (p ≤ 0.05) among cropping sequences at both locations with potato (Velum)-potato and C. africanus-potato sequences recording higher yields than potato monoculture or sorghum-potato.

DISCUSSION: Crop diversification increased soil organic carbon content, microbial diversity and enzyme activity. Overall, sorghum-potato effectively improved soil health and soil structure over time, better than the other cropping systems.},
}

@article {pmid42137817,
year = {2026},
author = {Farmakioti, I and Tegopoulos, K and Stylianopoulou, E and Siskos, N and Angelopoulou, L and Vasileiou, AR and Karagianni, E and Kandylas, D and Fragkiskatou, F and Pavlatou, C and Tsaroucha, A and Ypsilantis, P and Kourkoutas, Y and Kolovos, P and Skavdis, G and Grigoriou, ME},
title = {Genomic characterization and preclinical evaluation of the candidate probiotic strain Lactococcus cremoris FBMS_5810.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1812433},
pmid = {42137817},
issn = {1664-302X},
abstract = {This study presents a comprehensive genomic and preclinical evaluation of Lactococcus cremoris FBMS_5810, establishing its taxonomic identity, genomic uniqueness, and safety profile. Genomic analyses identified strain-specific genes linked to adhesion, colonization, and pathogen exclusion, aligning with previously observed in vitro probiotic properties. In vivo studies in healthy mice demonstrated that Lactococcus cremoris FBMS_5810 modulates gut microbiota composition. Specifically, the relative abundance of Muribaculaceae, Erysipelotrichaceae, and Streptococcaceae was significantly increased in the probiotic-treated group, whereas the relative abundance of Ruminococcaceae, Bacteroidaceae, Porphyromonadaceae, and Dehalobacteriaceae was decreased. Administration of Lactococcus cremoris FBMS_5810 was also associated with changes in intestinal gene expression: in the ileum, Tnf and Il1b expression increased, while in the cecum, Zo1 expression was elevated. These findings may indicate a role in supporting intestinal homeostasis and could be linked to reduced susceptibility to diet- and inflammation-related disorders. Overall, these results suggest that Lactococcus cremoris FBMS_5810 may be a useful candidate for further investigation in the development of health-oriented microbial products. By integrating genomic characterization with preclinical evaluation, this study not only highlights Lactococcus cremoris FBMS_5810 as a promising candidate but also provides a systematic approach for the identification and validation of probiotics, advancing both fundamental understanding and translational applications in molecular microbiology.},
}

@article {pmid42137872,
year = {2026},
author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC},
title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783141},
pmid = {42137872},
issn = {2296-861X},
abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.

METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120 days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.

RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p = 0.001) and d56 (p = 0.03) but did not result in significant change in WAZ (p = 0.69) or weight gain (p = 0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.

DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.

CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.},
}

@article {pmid42138066,
year = {2026},
author = {Allwang, M and Wipplinger, M and Akbarimoghaddam, P and Alonso-Roman, R and Cseresnyes, Z and Dietschmann, A and Wegner, V and Feile, A and Bachelot, Y and Warschinke, M and Hassan, MIA and Mittag, S and Huber, O and Hube, B and Gresnigt, MS and Figge, MT and Mosig, AS},
title = {Human Colitis-on-Chip Model Reveals Dual Roles of Butyrate in Epithelial and Macrophage Defense Against Candida albicans Tissue Invasion.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e00074},
doi = {10.1002/smll.202600074},
pmid = {42138066},
issn = {1613-6829},
support = {434385622/GR 5617/1-1//German Research Foundation/ ; //Exploration Grant of the Boehringer Ingelheim Foundation (BIS)/ ; //Free State of Thuringia and co-funded by the European Union/ ; 390713860//DFG Cluster of Excellence "Balance of the Microverse"/ ; FKZ: 13N15713 13N15716//DFG Cluster of Excellence "Balance of the Microverse"/ ; //Collaborative Research Center "PolyTarget"/ ; //Scholarship from the Interdisciplinary Center of Clinical Research of the Jena University Hospital/ ; },
abstract = {Microbial dysbiosis in inflammatory bowel disease (IBD) reduces intestinal butyrate levels, compromising epithelial barrier integrity and enabling overgrowth of opportunistic pathogens such as Candida albicans. Here, we present a human immunocompetent colitis-on-chip model (CooC) that mimics key features of inflamed gut mucosa, including DSS-induced epithelial damage and C. albicans tissue invasion. Using this model, we uncover dual protective roles of microbiota-derived butyrate: (i) stabilization of epithelial adherens junctions and promotion of epithelial renewal, thereby restricting fungal invasion; and (ii) modulation of macrophage function to enhance antifungal activity while attenuating inflammasome-mediated inflammation. Butyrate pretreatment preserves barrier function, limits fungal translocation, and promotes macrophage viability through the inhibition of histone deacetylase (HDAC) and the suppression of NLRP3 inflammasome activation. These findings position butyrate as a key metabolite in orchestrating epithelial-immune defense against fungal exacerbation in colitis, supporting its therapeutic and preventive potential in restoring mucosal resilience in IBD.},
}

@article {pmid42138097,
year = {2026},
author = {Kozajda, A and Miśkiewicz, E and Gawor, J and Gromadka, R},
title = {Bacteria and associated antibiotic resistance in air filter-derived biological material from utility vehicles at mechanical-biological treatment plants.},
journal = {International journal of occupational medicine and environmental health},
volume = {},
number = {},
pages = {},
doi = {10.13075/ijomeh.1896.02785},
pmid = {42138097},
issn = {1896-494X},
abstract = {OBJECTIVES: The study objective was to assess occupational exposure to bacteria and antimicrobial resistance genes (ARGs) present on air filters of utility vehicles used in the working environment of mechanical-biological treatment (MBT) facilities, in the context of workers health risks.

MATERIAL AND METHODS: The study was conducted in summer 2024 in 9 air filters from utility vehicles used in MBT plants in Poland. External filters were removed from the vehicle's ventilation system, packed and shipped according to instructions. From the duplicate filters samples DNA was isolated and high-throughput next-generation sequencing (NGS) was carried out. Bioinformatic data analysis was conducted to detect bacteria and ARGs in air filters' surfaces.

RESULTS: Totally, 34 bacterial taxa were detected in relative abundance ≥0.5%. The genera most frequently present at the highest relative abundances: Saccharomonospora, Thermobifida, Nocardiopsis, Pectobacterium, Aerococcus, Thermoactinomyces, Novibacillus and Streptomyces. Across all bacteria isolated from the analyzed filters, regardless of their relative abundance, a total of 91 taxa were classified into risk groups 2 or 3 (86 and 5 taxa, respectively). The most frequently detected ARGs were those encoding resistance to a single class of antibiotics (AAC(3)-VIIa, aadA2, ANT(6)-Ia, APH(3'')-Ia, APH(3'')-Ib, APH(6)-Id, cml, cmx, lnuA, lnuD, novA, parY, sul2, vanHF, vanJ, vanRA, vanRI, vanRO - each at least on 4 air filters). Antimicrobial resistance genes encoding multi antibiotic resistance were also detected: CRP, emtA, erm(34), erm(36), ermA, ermC, ermF, ermG, ermT, ermX, ernB, H-NS, mel, msrA, msrE, mtrA, optrA, ramA, ykkD - each at least on 1 air filter.

CONCLUSIONS: Despite the limited number of analyzed filters, the study demonstrated a high bacterial species diversity in the MBT plant environment. The MBT workers are exposed to bacteria with high pathogenic potential and to ARGs encoding resistance to antibiotics used exclusively in human medicine, used in human and veterinary medicine, and not intended for human use. Int J Occup Med Environ Health. 2026;39(2).},
}

@article {pmid42138193,
year = {2026},
author = {Ma, X and Zhao, Y},
title = {Gut‑brain axis in anesthesia and critical illness: Molecular crosstalk and its impact on delirium and outcome (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {1},
pages = {},
doi = {10.3892/ijmm.2026.5859},
pmid = {42138193},
issn = {1791-244X},
mesh = {Humans ; Critical Illness ; *Delirium/etiology/metabolism ; *Gastrointestinal Microbiome ; *Brain/metabolism ; *Anesthesia/adverse effects ; Animals ; },
abstract = {The gut‑brain axis (GBA) has emerged as a critical mediator of acute brain dysfunction, particularly postoperative delirium and sepsis‑associated encephalopathy, in surgical and critically ill patients. Anesthesia, surgical stress, and critical illness collectively disrupt gut microbiota composition and intestinal barrier integrity, leading to increased systemic translocation of microbial products. This process triggers neuroinflammation and compromises blood‑brain barrier function through defined molecular pathways, including alterations in microbe‑derived short‑chain fatty acids, tryptophan metabolites, and potent neuroimmune signaling via the LPS‑TLR4‑NF‑κB axis. The present review synthesizes current evidence on the molecular crosstalk within the GBA, highlighting how perioperative and intensive care interventions drive dysbiosis and subsequent neurological sequelae. Furthermore, it evaluates promising GBA‑targeted therapeutic strategies, including dietary modulation, biotherapeutics and pharmacological interventions, are evaluated for their potential to mitigate delirium and improve long‑term cognitive outcomes. A deeper understanding of these mechanisms is essential for developing novel preventive and therapeutic approaches in vulnerable patient populations.},
}

Humans
Critical Illness
*Delirium/etiology/metabolism
*Gastrointestinal Microbiome
*Brain/metabolism
*Anesthesia/adverse effects
Animals

@article {pmid42138225,
year = {2026},
author = {Jamieson, PE and Gu, I and Reichart, NJ and Maier, CS and Ho, E and Sharpton, TJ and Metz, TO and Bradley, R and Stevens, JF},
title = {Modulation of Microbiota-Derived Bile Acids Linked to Symptom Amelioration in Crohn's Disease: Insights From a Randomized Clinical Trial With Xanthohumol Supplementation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {10},
pages = {e70501},
doi = {10.1002/mnfr.70501},
pmid = {42138225},
issn = {1613-4133},
support = {R01 AT010271/NH/NIH HHS/United States ; R01 AT010271-02S1/NH/NIH HHS/United States ; S10OD026922/NH/NIH HHS/United States ; },
mesh = {Humans ; *Flavonoids/pharmacology/therapeutic use ; *Crohn Disease/drug therapy/microbiology ; *Bile Acids and Salts/metabolism ; *Propiophenones/pharmacology/therapeutic use ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Adult ; Dietary Supplements ; Middle Aged ; Feces/microbiology/chemistry ; Interleukin-10/blood ; Young Adult ; Humulus/chemistry ; },
abstract = {Xanthohumol (XN), a dietary flavonoid from hops (Humulus lupulus), possesses anti-inflammatory and microbiome-modulatory properties with potential therapeutic benefits for Crohn's disease (CD). To investigate the effects of XN on the gut environment in CD, we conducted a randomized, placebo-controlled clinical trial-the XN Microbiome and Signature (XMaS) trial (NCT4590508). 19 participants with clinically active CD completed the study. They were randomized to receive 24 mg/day of XN or placebo for 8 weeks, with clinical assessments at baseline and every 2 weeks. We assessed changes to Crohn's disease activity index (CDAI) scores, systemic inflammation, gut barrier function, profiling of microbial metabolism of XN, and gut microbiota composition and metabolism. Integration analysis of gut microbiota abundance, fecal metabolites, and inflammatory markers with CDAI scores revealed a pattern in which reductions in secondary bile acids and increases in IL-10 were associated with improved CDAI score in XN-treated individuals. These findings suggest that XN beneficially modulates the gut environment in CD by influencing microbial bile acid metabolism and host inflammatory response, thereby improving symptoms in individuals with severe innate immune activation.},
}

Humans
*Flavonoids/pharmacology/therapeutic use
*Crohn Disease/drug therapy/microbiology
*Bile Acids and Salts/metabolism
*Propiophenones/pharmacology/therapeutic use
Male
Female
*Gastrointestinal Microbiome/drug effects
Adult
Dietary Supplements
Middle Aged
Feces/microbiology/chemistry
Interleukin-10/blood
Young Adult
Humulus/chemistry

@article {pmid42138268,
year = {2026},
author = {Camps-Massa, P and Pérez-Mormeneu, J and Guevara-Nuñez, D and Saiz-Escobedo, L and Calatayud, L and González-Díaz, A and Sanllorente, A and Vicens-Zygmunt, V and Santos, S and Morros, R and Salvador-González, B and Domínguez, MÁ and Martí, S and , },
title = {Gut microbiome shift in long COVID: impact of disease and montelukast treatment.},
journal = {Journal of global health},
volume = {16},
number = {},
pages = {04164},
pmid = {42138268},
issn = {2047-2986},
mesh = {Humans ; *Cyclopropanes/therapeutic use ; *Sulfides/therapeutic use ; *Quinolines/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Acetates/therapeutic use ; *COVID-19/microbiology/complications ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; Adult ; Aged ; Longitudinal Studies ; *COVID-19 Drug Treatment ; },
abstract = {BACKGROUND: Long COVID-19 is a post-infectious syndrome with persistent symptoms that can involve multiple organ systems. Evidence suggests that SARS-CoV-2 infection may disrupt gut microbiome composition, potentially contributing to long-term effects. As treatment remains symptom-based, interest has grown in repurposing drugs like montelukast. However, non-antibiotic medications may also alter gut microbial communities, raising questions about their impact. Here, we compare gut microbiota between long COVID patients and healthy controls and examine how montelukast treatment affects microbial composition.

METHODS: We analysed stool samples from long COVID patients and healthy controls using 16S rRNA gene sequencing (Illumina MiSeq). We evaluate alpha (Shannon) and beta (Bray-Curtis) diversity, followed by relative abundance and linear discriminant effect size analysis, to identify differentially abundant taxa. This proof-of-concept study included a cross-sectional comparison and a longitudinal analysis of montelukast-treated patients vs. placebo.

RESULTS: Cross-sectional analysis revealed a significant structural reorganisation of the gut microbial community in long COVID patients, although overall species richness was largely maintained. Linear discriminant effect size analysis revealed that this architectural shift was driven by an enrichment of Firmicutes (Agathobacter and Faecalibacterium genera) in the long COVID group, while healthy controls were characterised by higher abundances of the phyla Verrucomicrobiota and Actinobacteriota, as well as genera Alistipes and Akkermansia. Longitudinal analysis demonstrated that the broader community structure remained stable in both groups; however, montelukast treatment led to a specific enrichment of the genus Dialister, suggesting targeted and potentially transient effects without disrupting the overall microbial landscape.

CONCLUSIONS: Long COVID is characterised by a significant restructure of the gut ecosystem. This qualitative dysbiosis reflects a shift in homeostatic balance, where the core microbial community remains present, but its proportions are altered. Short-term montelukast treatment shows a minimal impact on the microbial landscape, suggesting treatment does not further destabilise the gut environment. These findings highlight the specific and targeted nature of gastrointestinal involvement in long COVID.},
}

Humans
*Cyclopropanes/therapeutic use
*Sulfides/therapeutic use
*Quinolines/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Acetates/therapeutic use
*COVID-19/microbiology/complications
Male
Female
Cross-Sectional Studies
Middle Aged
SARS-CoV-2
Feces/microbiology
Adult
Aged
Longitudinal Studies
*COVID-19 Drug Treatment

@article {pmid42138670,
year = {2026},
author = {Khanna, S and Allegretti, JR and Hashash, JG and Feuerstadt, P},
title = {AGA Clinical Practice Update on Management of Clostridioides difficile Infection in Inflammatory Bowel Disease: Expert Review.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.03.008},
pmid = {42138670},
issn = {1528-0012},
abstract = {DESCRIPTION: Clostridioides difficile infection (CDI) remains a significant driver of disease flares and poor outcomes in patients with inflammatory bowel disease (IBD), leading to increased hospitalization, intensified or failed therapy, and higher surgical rates. Compared with the non-IBD population, patients with IBD face greater CDI risk and severity and higher recurrence risk, creating clinical dilemmas when considering antibiotic selection and the timing or necessity of IBD-related therapy adjustments. Emerging evidence highlights microbiota-based therapies such as unapproved fecal microbiota transplantation or US Food and Drug Administration-approved donor-derived therapies as a promising therapeutic avenue for recurrent CDI in patients with IBD, reflecting a growing emphasis on microbiome-directed interventions. This review examines the evolving literature, considering the diagnosis and management strategies and offering pragmatic guidance to optimize outcomes for patients with IBD challenged by concomitant CDI and recurrent CDI.

METHODS: This Expert Review was commissioned and approved by the American Gastroenterological Association (AGA) Institute Clinical Practice Updates Committee and the AGA Governing Board to provide timely guidance on a topic of high clinical importance to the AGA membership and underwent internal peer review by the Clinical Practice Updates Committee and external peer review through standard procedures of Gastroenterology. These practical Best Practice Advice statements were drawn from a review of the best available published evidence, including existing clinical studies, systematic reviews and practice guidelines, and expert opinion. Because a formal systematic review was not performed, these Best Practice Advice statements do not carry formal ratings of the quality of evidence or strength of the presented considerations. The focus is on the management of both CDI and IBD in patients with underlying IBD who develop CDI. Best Practice Advice Statements BEST PRACTICE ADVICE 1: In patients with IBD who have new or worsening diarrhea, CDI should be excluded, especially among those with colonic involvement, as they are at increased risk of CDI. Clinicians should consider and treat CDI in patients with end ileostomy or ileo-anal pouch anastomosis with worsening diarrhea. BEST PRACTICE ADVICE 2: In patients with IBD and suspected CDI, a multistep toxin-based assay should be used for diagnostic evaluation. BEST PRACTICE ADVICE 3: In patients with IBD and recent CDI who have been treated successfully with antibiotics, recurrent diarrhea should prompt retesting for CDI. BEST PRACTICE ADVICE 4: In patients with IBD who develop an initial episode of CDI, clinicians should preferentially use fidaxomicin or use vancomycin if fidaxomicin is unavailable or cost-prohibitive. Metronidazole should not be used. BEST PRACTICE ADVICE 5: Clinicians should strongly consider hospitalization for patients with IBD and CDI who demonstrate features of severe colitis or systemic toxicity (eg, more than 6 bowel movements per day, severe abdominal pain, marked leukocytosis, hemodynamic instability, or other evidence of sepsis). BEST PRACTICE ADVICE 6: When selecting an immunosuppressive therapy to treat IBD, no class or mechanism of action has a differential risk of CDI and, therefore, clinicians should choose the therapy that is best to treat the IBD. BEST PRACTICE ADVICE 7: In patients with IBD and acute CDI, concurrent treatment of IBD is critical and clinicians should continue therapy with the required immunosuppressive therapies (ie, immunomodulators, biologics, or small molecules). Steroids can also be used if deemed necessary while CDI is treated with antibiotics. BEST PRACTICE ADVICE 8: Clinicians should consider endoscopic evaluation for IBD activity and exclusion of concomitant cytomegalovirus infection if symptoms persist 48-72 hours after initiation of treatment for CDI. BEST PRACTICE ADVICE 9: Clinicians may consider loperamide in patients with improving inflammation and infection but ongoing diarrhea. BEST PRACTICE ADVICE 10: Clinicians should offer microbiome-based therapies (eg, fecal microbiota, live-jslm, fecal microbiota spores, live-brpk, or unapproved fecal microbiota transplantation) to patients with IBD with at least 1 recurrence of CDI to prevent future infection. BEST PRACTICE ADVICE 11: In patients with IBD, clinicians should not advise probiotics for primary or secondary prevention of CDI. BEST PRACTICE ADVICE 12: In patients with IBD and a history of CDI who are receiving systemic antibiotics, clinicians may consider oral vancomycin prophylaxis as secondary prevention.},
}

@article {pmid42138705,
year = {2026},
author = {Zhu, L and Wang, M and Zhang, X and Dou, T and Hua, H and Tang, X and Niu, X and Kou, Q and Chen, Y and Pan, M and Ma, B},
title = {Early supplemental feeding improves post-weaning growth restriction in lambs via the gastrointestinal-metabolic axis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0242125},
doi = {10.1128/aem.02421-25},
pmid = {42138705},
issn = {1098-5336},
abstract = {The weaning period often induces growth restriction in lambs due to gastrointestinal immaturity and dietary transition. Although early supplemental feeding (ESF) shows promise, its systemic mechanisms via the rumen microbiota-gut-metabolism axis remain incompletely understood. Sixty Tan lambs were assigned to a control group (suckling only), Trial Group I (free-access ESF from 10 days), and Trial Group II (free-access + forced isolation from 15 days). Growth performance, rumen fermentation, intestinal morphology, serum metabolites, and rumen microbiota were comprehensively analyzed. The supplemental feeding regimen in Trial Group I significantly improved body weight, average daily gain, and body size before and after weaning. Rumen butyrate and acetate concentrations increased markedly, with enrichment of beneficial microbiota (Bifidobacteriaceae and Sharpea). Intestinal villus height and villus-to-crypt ratio were enhanced in the jejunum and ileum. Regarding serum metabolism, lambs in both supplemental feeding groups showed significantly increased levels of albumin and urea and decreased total cholesterol. The activities of antioxidant enzymes (catalase, superoxide dismutase, and glutathione peroxidase) and the levels of oxidative products (malondialdehyde and hydrogen peroxide) in the serum of lambs from both supplemental feeding groups were significantly higher than those in the control group. Correlation analysis revealed positive associations between beneficial microbiota, fermentation parameters, intestinal development, and growth performance. ESF alleviates post-weaning growth restriction by remodeling the rumen microbiota, enhancing volatile fatty acid production, improving intestinal development, and optimizing host nutrient utilization. The free-access ESF regimen is recommended for efficient lamb production.IMPORTANCEThis study reveals that different regimens of early supplemental feeding differentially alleviate post-weaning growth restriction in lambs by distinctly remodeling the host's "rumen microbiota-gut-metabolism axis." The optimized regimen enriches beneficial rumen microbiota (e.g., Bifidobacteriaceae and Sharpea), increases key metabolite production (e.g., butyrate), and synergistically improves intestinal development and host protein/lipid metabolism, thereby elucidating the mechanism of growth promotion via microbe-host interactions. These findings advance the understanding of "nutrition-microbe-host" crosstalk in young ruminants and provide a theoretical framework for precision nutrition through microbiome modulation. The identified key microbes and metabolic functions offer potential targets for developing eco-friendly feed additives, aiding in reducing antibiotic reliance and promoting sustainable lamb production.},
}

@article {pmid42138826,
year = {2026},
author = {Chen, X and Shen, M and Zhang, R and Huang, Z and Niu, H and Yu, Q and Chen, Y and Pan, X and Rong, L and Wen, H and Yang, J and Xie, J},
title = {Sulfated Cyclocarya Paliurus Polysaccharide Sorchestrates the Gut Microbiome to Mobilize a Host-Derived 12-HEPE Against Ulcerative Colitis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75681},
doi = {10.1002/advs.75681},
pmid = {42138826},
issn = {2198-3844},
support = {2023YFF1104001//National Key Research and Development Program of China/ ; 82460642//National Natural Science Foundation of China/ ; },
abstract = {Despite extensive evidence supporting the therapeutic potential of natural product-derived compounds in Ulcerative colitis (UC), their precise mechanisms have yet to be fully elucidated. In this study, structurally modified Cyclocarya paliurus polysaccharide (CP) derivatives were evaluated in a dextran sulfate sodium (DSS)-induced UC mouse model. Among the variants tested, sulfated Cyclocarya paliurus polysaccharide (SCP) emerged as the most therapeutically potent. SCP administration markedly attenuated colitis severity, as evidenced by relieved disease symptoms and reinforced intestinal barrier function. Mechanistically, SCP restored gut microbial homeostasis by enriching beneficial Bacteroidetes and enhancing short-chain fatty acids (SCFAs) production. This remodeled microbial ecosystem orchestrates the upregulation of host-derived 12-hydroxyeicosapentaenoic acid (12-HEPE), which exerts anti-inflammatory effects via direct inhibition of Toll-like receptor 4 (TLR4) signaling. The gut microbiota's functional relevance was substantiated by fecal microbiota transplantation and antibiotic-mediated exhaustion studies. Notably, the therapeutic benefits of 12-HEPE were abrogated upon co-administration of a TLR4 agonist, confirming its target specificity. Elevated serum 12-HEPE levels were observed in a human UC cohort, implying a potential compensatory immunoregulatory response. Our findings elucidate a novel microbiota-host interaction axis wherein SCP alleviates UC by modulating the gut microbiota to enhance endogenous 12-HEPE production, thereby suppressing TLR4-mediated inflammation.},
}

@article {pmid42138982,
year = {2026},
author = {Pereira, VH and Cassiano, GH and Ferreira, PHN and Abreu, LGF and Sousa, JES and Carazzolle, MF and Pereira, GAG and Silva, NV},
title = {An integrated microbiological analysis of the soil and rhizosphere of Agave spp. under minimum technological input farming systems.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
pmid = {42138982},
issn = {1465-2080},
mesh = {*Agave/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Agriculture/methods ; Bacteria/classification/isolation & purification/genetics ; Crops, Agricultural/microbiology ; },
abstract = {The expansion of arid and semi-arid regions, consequent to the intensification of desertification processes attributable to global warming, exerts a deleterious effect on the agricultural production of energy crops, with current estimates indicating that a further 23% of global agricultural areas will suffer from desertification by 2100, precipitating crises in these sectors. Agave species have the capacity to thrive in these marginal environments characterized by aridity and elevated temperatures. These plants can serve as a source of biomass for the production of biofuels, a process that mitigates the environmental impacts of the transport sector while promoting the utilization of drylands, thereby eliminating competition with food crops. Given the paucity of knowledge regarding the soil microbiota and rhizosphere in minimal technological input Agave plantations, the objective of this study was to evaluate the microbiological and chemical soil properties of Agave sisalana and Agave hybrids (H11648 and H400f) farming systems. The analyses, which were carried out using microbial quantification, enzyme stoichiometry and enzymatic vector calculations, demonstrated that the microbiome of these plants is active and well-structured in terms of nutritional acquisition. It was observed that the Agave fields' microbiome is very similar to that of the native vegetation. This finding suggests that the soil and rhizosphere microbiota are healthy and stable in the Agave fields evaluated, even with the implementation of agronomic exploitation models, as the chemical analysis of the soil reveals that all measured parameters are consistent with those of soils suitable for crop production. These observations persist even in long-established Agave plantations of varying ages that have never received any type of implement or soil correction. Thus, the integration of the chemical and biological data through principal component analysis, redundancy analysis and Permutational Multivariate Analysis of Variance (PERMANOVA) enabled the differentiation of the soil among the three Agave species, which shows the influence of the plant genotype on its microbiota.},
}

*Agave/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
*Soil/chemistry
Microbiota
Agriculture/methods
Bacteria/classification/isolation & purification/genetics
Crops, Agricultural/microbiology

@article {pmid42139081,
year = {2026},
author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Dietary Niches Drive Microbial Community Assembly, Network Reorganization, and Symbiont Evolution in Freshwater Fish Gut Microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag125},
pmid = {42139081},
issn = {1751-7370},
abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.},
}

@article {pmid42139085,
year = {2026},
author = {Sidhom, J and Balla, SB and Tadakamadla, SK and Tadakamadla, J},
title = {The Association Between Self-Reported Nicotine Vaping and the Human Oral Microbiome: A Systematic Review.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntag103},
pmid = {42139085},
issn = {1469-994X},
abstract = {INTRODUCTION: Nicotine Vapes have experienced a rise in their popularity, and our understanding of how vapes affect our oral microbiome remains to be reviewed. This systematic review explores whether the use of vapes is associated with measurable alterations in the diversity and taxonomic composition of the oral microbiome compared to non-vapers or conventional cigarette smokers.

METHODS: A comprehensive and systematic search of 6 databases was meticulously conducted, covering published literature up to the end of August 2024. The data was then extracted and underwent a qualitative analysis. Studies' risk of bias was assess using Newcastle Ottawa Scale Eligible studies needed to have a comparison group of either non-smokers or tobacco users or both and a group of sole e-cigarette users.

RESULTS: The search yielded 18 articles, with sixteen being cross-sectional and the remaining two were cohort studies. There were 1418 participants across the studies, ranging from 30-125 participants in each study. Majority of the included literature indicated e-cigarettes can alter the taxonomic composition and diversity of their user's oral microbiome.

CONCLUSIONS: Vaping was found to be associated with changes in oral microbiome. Since, the majority of the existing literature relied on self-reporting to see if participants were sole vapers, and mainly focused on bacterial genera, the exact impact of these changes are difficult to ascertain. However, the existing literature demonstrates a relationship in a few bacterial genera associated with periodontal disease among e-cigarette users, highlighting the need for further comprehensive studies with sound methodological approach to recruit sole e-cigarette users.

IMPLICATIONS: This study concludes that nicotine vapes do have a demonstratable impact on the oral microbiome that is unique to vapes. E-cigarette use may be associated with an increase periodontal pathogens which may predispose e-cigarette users to worse periodontal disease, however, further research is required.},
}

@article {pmid42139269,
year = {2026},
author = {Wein, H and Iglesias-Moreno, P and Apostolov, A and Salumets, A and Muzzio, DO and Sola-Leyva, A},
title = {Bacterial Extracellular Vesicles: New Hype or Hope to Explain Reproductive Host-Microbiota Interactions.},
journal = {Journal of extracellular vesicles},
volume = {15},
number = {5},
pages = {e70296},
pmid = {42139269},
issn = {2001-3078},
support = {PSG1082//Estonian Research Council/ ; PRG1076//Estonian Research Council/ ; 2024-02530//Vetenskapsrådet/ ; 101236395//Horizon Europe / Marie Skłodowska-Curie Staff Exchange/ ; TK214//Estonian Ministry of Education and Research/ ; 101120075//HORIZON EUROPE Health/ ; NNF24OC0092384//Novo Nordisk Fonden/ ; MU 4404/3-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Extracellular Vesicles/metabolism ; Female ; Pregnancy ; *Microbiota ; *Host Microbial Interactions ; Animals ; *Reproduction ; *Bacteria/metabolism ; },
abstract = {Rapid advances in microbiome research are transforming our understanding of human health and disease, with growing focus on the female reproductive tract as a critical but understudied niche. Evidence for a local microbiome largely derives from bacterial nucleic acid detection; however, the biological relevance of these signals remains debated, with whether they reflect viable microbial communities, transient colonisation, or mere microbial remnants with immunomodulatory effects. Bacterial extracellular vesicles (BEVs) have emerged as pivotal mediators of host-microbiota crosstalk. Their small size enables them to traverse tissue barriers, enter systemic circulation and access barrier-protected anatomical sites like the placenta, thereby extending their biological reach beyond the site of origin. Although BEVs have been extensively characterised in the context of gastrointestinal, respiratory and systemic diseases, their relevance within the reproductive tract remains insufficiently defined. Understanding whether BEVs contribute to processes such as endometrial receptivity, gamete interaction, embryo implantation and immune tolerance in early pregnancy may reveal novel mechanisms of reproductive physiology and pathology. Furthermore, unravelling the role of BEVs could help resolve the ongoing debate regarding the existence of a functional upper reproductive tract (URT) microbiota, reframing it in terms of microbial activity rather than microbial presence alone. This review synthesises the limited but growing body of evidence on BEVs in the reproductive tract, with a particular emphasis on their potential influence on female fertility and early pregnancy outcomes. We also outline the major methodological challenges, including the discrimination of BEVs from host-derived extracellular vesicles (EVs), the technical limitations of current detection approaches and the risk of contamination in low-biomass environments that complicate research in this field. Finally, we highlight conceptual frameworks and future research directions needed to establish BEVs as important players in reproductive biology and to harness their diagnostic and therapeutic potential in reproductive medicine.},
}

Humans
*Extracellular Vesicles/metabolism
Female
Pregnancy
*Microbiota
*Host Microbial Interactions
Animals
*Reproduction
*Bacteria/metabolism

@article {pmid42139619,
year = {2026},
author = {Dorohavtseva, HA and Dorofieiev, AE and Myroshnychenko, MS},
title = {Clinical, endoscopic, morphological and microbiological characteristics of diverticular disease in patients with metabolic disorders.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {4},
pages = {803-810},
doi = {10.36740/WLek/220666},
pmid = {42139619},
issn = {0043-5147},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Aged ; *Diverticular Diseases/microbiology/pathology/complications ; *Obesity/complications ; Adult ; Intestinal Mucosa/pathology/microbiology ; *Metabolic Diseases/complications ; Overweight/complications ; },
abstract = {OBJECTIVE: Aim: The aim of the study was to identify the clinical course and endoscopic activity features in patients with uncomplicated diverticular disease (UDD) associated with diabetes mellitus (DM), overweight, and obesity and perform an analysis of the gut microbiome and morphological characteristics of the colonic mucosa in such patients.

PATIENTS AND METHODS: Materials and Methods: 259 patients with UDD, hospitalized in the Department of Gastroenterology of Feofaniya Clinical Hospital of the State Administration of Affairs during the period of 2020-2024, were included in the study. Among all patients with DD included in the study, 43 had no metabolic disorders (MD) (DM, overweight, obesity), while 216 presented with varying degrees of MD. All patients underwent total colonoscopy with assessment of endoscopic activity of diverticular inflammation using the Diverticular Inflammation and Complication Assessment (DICA) score. The clinical course of DD was evaluated according to the classification proposed by the German Society of Gastroenterology, Digestive and Metabolic Diseases and the German Society of General and Visceral Surgery in 2021. The microbiome analysis was conducted only in 172 patients who had the financial means to undergo this test. During endoscopic examination of the colon in all patients, mucosal biopsies were obtained from the diverticular orifice. Histological, histochemical, and immunohistochemical methods were used. The obtained digital indicators in the groups were analyzed using statistical methods.

RESULTS: Results: This study evaluated clinical, endoscopic, morphological, and microbiological characteristics of DD in patients with metabolic disorders. A recurrent course of diverticular inflammation was observed more frequently in patients with metabolic dysfunctions. Endoscopic assessment of inflammatory activity correlated with histological changes of colon mucosa and alterations in mucin expression (MUC2 and MUC4). Microbiological analysis revealed a reduction in butyrate-producing flora (Akkermansia muciniphila, Faecalibacterium prausnitzii) with predominance of Bacteroidetes in metabolic disorder patients.

CONCLUSION: Conclusions: The clinical, morphological, microbiological and endoscopic features of DD identified by the authors highlight pathophysiological links between metabolic dysfunction (DM, overweight, obesity) and DD progression.},
}

Humans
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Colonoscopy
Aged
*Diverticular Diseases/microbiology/pathology/complications
*Obesity/complications
Adult
Intestinal Mucosa/pathology/microbiology
*Metabolic Diseases/complications
Overweight/complications

@article {pmid42139623,
year = {2026},
author = {Khudhair, HM and Alhamdani, ASH and Al Tameemi, AMH},
title = {Microbiology of dental decay and periodontal disease: A review.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {4},
pages = {829-846},
doi = {10.36740/WLek/216932},
pmid = {42139623},
issn = {0043-5147},
mesh = {Humans ; *Periodontal Diseases/microbiology/therapy ; *Dental Caries/microbiology/therapy ; Biofilms ; Porphyromonas gingivalis/pathogenicity ; Mouth/microbiology ; },
abstract = {OBJECTIVE: Aim: This review attempts to examine the microbiology, pathogenesis and current therapeutic approaches of dental caries and periodontal diseases with a special focus on the role of polymicrobial biofilms, the host-microbe interaction and the major pathogenic species involved in disease progression.

PATIENTS AND METHODS: Materials and Methods: A thorough literature review was performed using major scientific databases such as PubMed, Scopus, Web of Science and Google Scholar. Studies that were published between 2000 and 2025 were included. Relevant experimental, clinical and review articles that focused on the etiology, microbial composition, virulence mechanisms, host immune responses and therapeutic approaches of dental caries and periodontal disease were analyzed.

CONCLUSION: Conclusions: The oral cavity harbors over 700-800 bacterial species, of which the primary cariogenic pathogen is Streptococcus mutans and Porphyromonas gingivalis has been implicated as a major cause of periodontal disease. Dental caries progression is mostly attributed to acid production and demineralization of enamel, whereas periodontal disease is a result of dysbiotic shift in the subgingival microbiome with destructive host inflammatory responses. The "red complex" (P. gingivalis, Treponema denticola and Tannerella forsythia) has a high degree of synergistic virulence in advanced periodontitis. Biofilm formation, production of extracellular polysaccharide (EPS) matrix, quorum sensing and immune components (neutrophils, macrophages and matrix metalloproteinases or MMPs) are all factors that contribute to disease formation. Prevention strategies include oral hygiene measures, fluoride exposure, dietary modification, and antimicrobial agents, whereas treatment measures include mechanical debridement, systemic antibiotics, antimicrobial peptides, probiotics, and photodynamic therapy. Dental caries and periodontal diseases are the result of complex interactions between polymicrobial biofilms and immune responses by the host. A better understanding of the microbial ecology, virulence pathways and host-pathogen interactions is crucial in the process of improving prevention and treatment. Advances in targeted antimicrobial therapies and innovative therapeutic approaches hold promise for enhancing global oral health outcomes.},
}

Humans
*Periodontal Diseases/microbiology/therapy
*Dental Caries/microbiology/therapy
Biofilms
Porphyromonas gingivalis/pathogenicity
Mouth/microbiology

@article {pmid42139793,
year = {2026},
author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG},
title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.},
journal = {Veterinary microbiology},
volume = {319},
number = {},
pages = {111070},
doi = {10.1016/j.vetmic.2026.111070},
pmid = {42139793},
issn = {1873-2542},
abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.

METHODS: Stool samples from Danish diary calves (n = 32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon α-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3 +). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.

RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.

CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.},
}

@article {pmid42140024,
year = {2026},
author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L},
title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.},
journal = {International journal of food microbiology},
volume = {457},
number = {},
pages = {111847},
doi = {10.1016/j.ijfoodmicro.2026.111847},
pmid = {42140024},
issn = {1879-3460},
abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.},
}

@article {pmid42140124,
year = {2026},
author = {Lu, Y and Wu, Y and Zhang, H and Gao, D and Xie, H and Fu, S and Wang, H and Li, X},
title = {Multi-omics and in silico assessment of ecological risks posed by agrochemical coatings: Disruption of rhizosphere stress signaling and induction of bulb rot in Fritillaria cirrhosa.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120276},
doi = {10.1016/j.ecoenv.2026.120276},
pmid = {42140124},
issn = {1090-2414},
abstract = {Agrochemical seed coatings are widely used to control soil-borne pathogens. However, their unintended ecological effects on rhizosphere interactions and plant health remain unclear. Here, we combined a field transplantation trial, multi-omics analyses, and molecular docking to investigate the effects of fungicide-based seed coatings on the rhizosphere microecology of Fritillaria cirrhosa.The field trial showed that coating treatment unexpectedly increased bulb rot incidence by 2.8-fold compared with untreated controls (P < 0.001). Multi-omics analyses further indicated that coating application disrupted rhizosphere microecology, as evidenced by a 25.1% decline in bacterial diversity, reduced network complexity, and enrichment of pathogenic Fusarium species. Metabolomic analysis revealed the accumulation of exogenous xenobiotics along with downregulation of pyrimidine metabolism pathway, suggesting altered plant-microbe chemical communication. Stress-related metabolites, including salicylic acid (SA), L-carnitine, and ethylmalonate, accumulated, whereas key signaling molecules, such as adenosine, monoacylglycerol (18:3), Lysophosphatidylethanolamine 15:1 were depleted (0.03-fold) in the treatment group. Moreover, the decrease in jasmonic acid coupled with an increase in SA suggests immune hijacking associated with necrotrophic pathogens such as Fusarium, a pathological cascade further supported by the accumulation of mycotoxins such as T-2 triol. Cross-domain network and molecular docking analyses further clarified interactions between hub metabolites and the microbial community. Notably, adenosine exhibited strong binding affinities (< -6.0 kcal/mol) to both plant defense-related proteins (JOX2 and CotA laccase) and fungal pathogenicity targets, indicating a key role for endogenous plant defense signals in maintaining rhizosphere ecological balance. Collectively, these findings provide robust correlative evidence linking agrochemical seed coatings to rhizosphere microecological dysbiosis, characterized by reduced metabolite-mediated recruitment of beneficial microbiota and disrupted interkingdom signaling. This pathogen-favoring environment highlights the often-overlooked ecological impacts of seed coatings and underscores the urgent need for microbiome-compatible disease management strategies in perennial bulbous crop production.},
}

@article {pmid42140291,
year = {2026},
author = {Ojeda-Martinez, D and Boter, M and Ortego, F and Santamaria, ME},
title = {Unveiling CAZyme modularity patterns: Comparative genomics links domain architecture to arthropod diets and life histories.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152547},
doi = {10.1016/j.ijbiomac.2026.152547},
pmid = {42140291},
issn = {1879-0003},
abstract = {Carbohydrate-active enzymes (CAZymes) are proteins that assemble, remodel, and depolymerize complex carbohydrates. They are ubiquitous across the tree of life, underpinning energy capture, cell-wall architecture, microbiome interactions, and host-pathogen dynamics. CAZymes are modular in structure and function, being tightly related to the overall enzyme architecture. Domain architecture constrains folding, substrate range, and integration into metabolic pathways. Arthropods, the most species-rich animal phylum, offer a powerful system to study enzymatic modularity because their enzymatic machineries must function in extremely diverse ranges of diet, niche, and abiotic conditions. Here we built a genome-scale framework to characterize CAZyme modular organization across Arthropoda and to test how domain architecture is influenced by diets, life histories and clades while revealing emergent functional relationships. We find that unimodular architectures dominate CAZyme repertoires, while multimodular and class-exclusive arrangements remain rare but highly variable. We identify herbivory as responsible for the discrimination on three CAZyme structural strategies (saprophagous, leaf-stem-root, and pollen-nectar feeders) differing in class composition, modular complexity, and catalytic emphasis. Correlation and co-occurrence analyses at genomic and protein levels show that expansions of glycosyltransferases, glycoside hydrolases, carbohydrate-binding modules, and auxiliary activities are tightly coupled, especially in myriapods and crustaceans, and that intra-protein networks of CAZyme families are denser in hexapods, holometabolans, and herbivores. Within these networks, GT2 and hydrolytic domains occupy central positions in co-occurrence clusters. Together, our findings indicate that arthropod CAZymes evolve as integrated macromolecular systems whose modularity and class balance track ecological demands, providing a scalable framework for engineering CAZyme networks for biotechnological and pest-management applications.},
}

@article {pmid42140378,
year = {2026},
author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA},
title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {590},
number = {},
pages = {121086},
doi = {10.1016/j.cca.2026.121086},
pmid = {42140378},
issn = {1873-3492},
abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.},
}

@article {pmid42140385,
year = {2026},
author = {Li, Y and Zhang, J and Liu, H and Noman, M and Rizwan, MA and Isiaka, ID and Chen, H and Li, W and Zhao, N and Li, Y and Sun, Y and Lu, X and Liu, D and Yan, Y},
title = {Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.05.002},
pmid = {42140385},
issn = {1995-820X},
abstract = {Respiratory syncytial virus (RSV) bronchiolitis is the leading cause of hospitalization in infancy and exhibits pronounced age-dependent clinical heterogeneity. Fever becomes increasingly prevalent with age, yet whether febrile representation reflects a uniform inflammatory and immune phenotype across infancy remains unclear. In this prospective cohort of infants hospitalized with RSV bronchiolitis, we performed an integrated analysis of clinical features, pharyngeal microbiome composition, host transcriptomic profiles, and host-microbe interaction networks, with particular attention to age-related variation in fever-associated patterns. Clinically, fever prevalence exhibited a strong age-dependent increase across infancy. Correspondingly, canonical correspondence analysis identified age and fever as dominant gradients related to variation in both pharyngeal microbiome composition and host gene expression. Although no significant age-dependent correlations were observed at the global microbial and host transcriptomic levels in the fever-age interaction model, distinct patterns of microbial and host responses related to fever were observed across different age groups. Specifically, ranked gene set enrichment analysis indicated that febrile infants in early infancy showed relative attenuation of host defense-related programs, whereas older infants showed stronger enrichment of antiviral and inflammatory effector pathways, with more selective regulatory and signaling-associated patterns in late infancy. Integrated host-microbe network analysis further delineated a coherent developmental trajectory of fever-associated interaction architectures, evolving from densely interconnected regulatory networks in early infancy to modular, selectively coupled, host-centered configurations with advancing age. Together, febrile responses in RSV bronchiolitis should not be interpreted as a uniform biological phenotype across infancy and support age-aware interpretation of fever in pediatric RSV infection.},
}

@article {pmid42140394,
year = {2026},
author = {Linton, S and Sjaarda, C and Hossenbaccus, L and Davis, A and Greenlaw, J and Douchant, K and Thiele, J and Garvey, S and Botting, H and Steacy, LM and Sheth, PM and Ellis, AK},
title = {Characterizing the Nasal Microbiome Using a Nasal Allergen Challenge Model.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.05.003},
pmid = {42140394},
issn = {1097-6825},
abstract = {BACKGROUND: The role of the nasal microbiome in allergic rhinitis (AR), particularly following direct allergen exposure using a controlled model, remains incompletely understood. Understanding microbiome dynamics after allergen challenge could provide insights into AR pathophysiology.

OBJECTIVE: To evaluate nasal microbiome changes following a nasal allergen challenge (NAC) with ragweed pollen extract in individuals with ragweed-induced AR compared to non-allergic controls.

METHODS: Nineteen ragweed-allergic and twelve non-allergic participants completed an out-of-season NAC. Middle meatus and the adjacent nasal cavity secretions were collected at baseline and 6, 24, and 48 hours post-challenge. Microbial composition was characterized using 16S rRNA sequencing. Alpha diversity was assessed using Shannon and Chao1 indices, and beta diversity using Bray-Curtis dissimilarity with principal coordinate analysis. Ragweed-specific IgE (sIgE), total IgE (tIgE), and Staphylococcus aureus nasal carriage were also evaluated.

RESULTS: Nasal microbial community composition differed according to biological sex (beta diversity P = 0.001) and S. aureus carriage (P = 0.015). However, allergic status and NAC exposure had no significant effect on alpha or beta diversity over time. Genus-level differences between allergic and non-allergic participants emerged at 24 and 48 hours post-challenge (P = 0.028 and P = 0.0062), with greater relative abundance of Streptococcus and Veillonella observed in non-allergic individuals. Stratification by sIgE demonstrated significant differences in microbial community structure (P = 0.001), with higher sIgE levels associated with increased relative abundance of Streptococcus, Rothia, and Neisseria. Higher tIgE levels were also associated with distinct microbial community profiles and reduced Shannon diversity.

CONCLUSION: The nasal microbiome remained stable following acute allergen exposure despite clinical responses, while host factors including IgE levels, sex, and S. aureus carriage were associated with differences in microbial community composition.},
}

@article {pmid42140492,
year = {2026},
author = {Corcione, S and Benech, N and Kuijper, E and , },
title = {Microbiome science at a turning point: from descriptive ecology to clinical decision-making in infectious diseases.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.05.017},
pmid = {42140492},
issn = {1469-0691},
}

@article {pmid42140743,
year = {2026},
author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC},
title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {5},
pages = {},
doi = {10.1136/jitc-2025-014702},
pmid = {42140743},
issn = {2051-1426},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; },
abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.

METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1×10[11] or 4×10[11] colony forming unit (CFU)/day) plus pembrolizumab (200 mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.

RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-naïve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-naïve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95% CI 5.6 to not reached) and 1.8 months (95% CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.

CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-naïve metastatic NSCLC with PD-L1 >50%.

TRIAL REGISTRATION NUMBER: NCT05877430.},
}

Humans
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Female
Male
Middle Aged
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology
Aged
*Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology
*Melanoma/drug therapy/pathology
*Lung Neoplasms/drug therapy/pathology
Mice
*Head and Neck Neoplasms/drug therapy/pathology
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
Animals
Adult

@article {pmid42140787,
year = {2026},
author = {Singh, N and Srivastav, M},
title = {Comment on "Distinct gut microbiota signatures and predicted lipid metabolism pathways in Taiwanese patients with acute versus chronic coronary syndromes".},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.05.046},
pmid = {42140787},
issn = {0929-6646},
}

@article {pmid42140850,
year = {2026},
author = {Fagundes, D and Costa, LMS and Cagliari, A and de Vargas, DP and Rieger, A},
title = {Microbial Community Shifts and Plant Performance Improvements Driven by Bacillus firmus in Pampa Agroecosystems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70315},
pmid = {42140850},
issn = {1758-2229},
mesh = {*Bacillus/physiology ; *Soil Microbiology ; *Microbiota ; Rhizosphere ; *Glycine max/growth & development/microbiology/parasitology ; Plant Roots/growth & development/microbiology ; Animals ; Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Nematoda ; Ecosystem ; Soil ; },
abstract = {The impact of Bacillus firmus-based bionematicides on rhizosphere microbiota and plant performance remains poorly understood in complex agroecosystems. This study evaluated the effects of B. firmus application on soil microbial communities, nematode dynamics, and soybean productivity in the Pampa biome. Our results demonstrate that B. firmus significantly modulates the composition and diversity of soil microbiota, with effects varying across locations and over time. Treated areas exhibited shifts in bacterial communities, including increased abundance of beneficial taxa, while fungal diversity tended to decrease, likely due to the combined effect of the fungicide used in seed treatment. Despite persistent populations of target nematodes such as Pratylenchus brachyurus and Heterodera glycines, treated areas showed reduced root infestation in specific stages and locations. Importantly, the application of B. firmus consistently enhanced soybean shoot and root growth, resulting in productivity gains of 6%-7% across all sites. These findings reveal that B. firmus not only contributes to plant growth promotion but also induces significant, yet context-dependent, shifts in rhizosphere microbial communities. The study highlights the ecological complexity of microbial responses to biocontrol agents and underscores the importance of integrating microbiome dynamics into sustainable nematode management strategies in agroecosystems.},
}

*Bacillus/physiology
*Soil Microbiology
*Microbiota
Rhizosphere
*Glycine max/growth & development/microbiology/parasitology
Plant Roots/growth & development/microbiology
Animals
Fungi/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Nematoda
Ecosystem
Soil

@article {pmid42140946,
year = {2026},
author = {Zheng, R and Li, Y and Shang, P and Shen, Y and Nan, Z and Duan, T},
title = {Anthracnose drives assembly of phyllosphere epiphytic bacterial communities to increase disease resistance.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00991-z},
pmid = {42140946},
issn = {2055-5008},
support = {grant no. 2023-NK-147//the Fundamental Research Funds for the Leading Scientist Project of Qinghai Province/ ; },
abstract = {The phyllosphere microbiome plays crucial roles in plant health, but evidence of 'cry for help' strategy in the face of pathogen attack in the phyllosphere remains limited, particularly for the microbiomes of distinct leaf ecological niches. We investigated whether foliar pathogen anthracnose (Colletotrichum lentis) influenced the assembly and functions of microbiomes in epiphytic and endophytic niches of the phyllosphere of common vetch (Vicia sativa) leaves. We also evaluated synthetic microbial communities (SynComs), including representatives of disease-associated strains, for pathogen protection. Anthracnose mediated the deterministic assembly process of epiphytic bacterial and endophytic fungal communities, and increased the complexity of bacterial co-occurrence networks. Iron competition and antifungal genes were also enriched in the epiphytic bacteria, which produce siderophores and degrade fungal cell walls to counteract pathogens. SynComs of beneficial epiphytic bacteria partially protect hosts by regulating bacterial interactions and inducing host immune responses. These findings suggest that disease drives the deterministic assembly of distinct phyllosphere microbiomes, their diversity and their function. Moreover, SynComs from the epiphytic niche can confer host plant disease resistance.},
}

@article {pmid42140950,
year = {2026},
author = {Garrido-Castro, AC and Graham, N and Li, KX and Bi, L and Crowdis, J and Bi, K and Park, J and Pastorello, R and Li, Y and Gupta, H and Kuntz, T and Petry, R and Pasquina, LW and Patel, A and Lange, P and DiLullo, M and Attaya, V and Frey, AM and Childress, MA and Wesolowski, R and Sinclair, N and Sinclair, S and Lo, S and Tung, N and Faggen, M and Kaufman, PA and Block, CC and Walsh, J and Toke, M and Chen, W and Wucherpfennig, KW and Tian, Y and Williams, AJ and Mukhopadhyay, S and Dasgupta, T and Schnitt, S and Cherniack, AD and Barroso, R and Ligibel, J and Lin, NU and Mittendorf, EA and Tayob, N and Van Allen, E and Tolaney, SM},
title = {Carboplatin with or without nivolumab in metastatic triple-negative breast cancer: a randomized phase II trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73085-1},
pmid = {42140950},
issn = {2041-1723},
abstract = {This multi-institutional randomized phase II clinical trial (NCT03414684) investigated the efficacy and safety of carboplatin plus nivolumab compared to carboplatin in metastatic triple-negative breast cancer (mTNBC). The primary endpoint was progression-free survival (PFS) in a modified intention-to-treat (mITT) population of patients with chemotherapy-naïve (i.e., first-line) mTNBC. Secondary endpoints included overall survival (OS), confirmed objective response rate, confirmed clinical benefit rate, time to and duration of confirmed objective response, safety, and tolerability. Clinical outcomes were evaluated in the PD-L1-positive subgroup (≥ 1% immune cells; SP142 clone) per central review. Biospecimens were collected for correlative analyses. 75 patients were enrolled and treated between 2/2018-9/2020. Among the mITT population (n = 62), median PFS was 4.2 months with carboplatin plus nivolumab vs 5.5 months with carboplatin. Median OS did not significantly differ between arms (16.8 vs 11.1 months, respectively). In PD-L1-positive mTNBC patients (n = 24), median PFS was 8.3 vs 4.7 months; median OS was 17.6 vs 10.7 months. Grade ≥3 adverse events occurred in 56.8% of patients in the combination arm and 65.8% in the carboplatin arm. Carboplatin plus nivolumab did not significantly improve PFS compared to carboplatin in patients overall; however, a trend toward improved outcomes was observed in PD-L1-positive mTNBC patients. High mutational burden, interferon-gamma signaling, early circulating tumor DNA reduction, low baseline serum thymidine kinase activity, and urea cycle dysregulation in the microbiome emerged as potential predictors of response to immune checkpoint inhibitors with platinum.},
}

@article {pmid42141277,
year = {2026},
author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G},
title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {42141277},
issn = {2662-1355},
abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.},
}

@article {pmid42141284,
year = {2026},
author = {},
title = {Even mild blows to the head disrupt the microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42141284},
issn = {1476-4687},
}