@article {pmid42090762,
year = {2026},
author = {Barnabei, G and Destri, D and Franco-Benito, M and Cebrian-Aldana, M and Mishra, A and Gil-Guerrero, S and Castilla-Alcantara, JC and Velasco-Arroyo, B and Barros-Garcia, R and Di Mambro, R and Bertelloni, N and Di Gregorio, S},
title = {Region-specific patterns of soil bacterial communities' adaptation to hexachlorocyclohexane contamination.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142224},
doi = {10.1016/j.jhazmat.2026.142224},
pmid = {42090762},
issn = {1873-3336},
abstract = {Hexachlorocyclohexane (HCH) is a persistent organochlorine pollutant whose attenuation at former production sites relies on microbial degradation. The canonical lin pathway, predominantly associated with Sphingomonadaceae, is considered the main aerobic route for HCH transformation, yet its environmental distribution remains limited. We investigated soil bacterial communities and enrichment-derived bacterial consortia from three historically contaminated sites in Germany, Italy, and Spain using HCH depletion assays, 16S rDNA metabarcoding, and functional inference, based on a curated BIOSYSMOdb dataset developed by the BIOSYSMO project. Based on the ASL-level functional inference, the Spanish samples uniquely encoded a complete lin pathway restricted to Sphingobium sp., whereas German and Italian communities harboured respectively partial (LinB-C) or single-step (LinB) modules. Despite these differences, efficient depletion of all HCH isomers occurred across all enrichment cultures. Core-microbiome and differential-abundance analyses identified several non-Sphingomonadaceae taxa, including Stenotrophomonas, Pseudomonas, Achromobacter, Pseudolabrys, and Cupriavidus, which consistently increased during selective enrichment and likely contribute to HCH depletion. Overall, our findings suggest that effective HCH degradation is not restricted to the canonical lin pathway nor to Sphingomonadaceae but it might be mediated also by diverse soil bacteria via alternative lin-independent mechanisms. These results broaden the known ecological and functional landscape of HCH biodegradation and support the exploration of non-Sphingomonadaceae taxa for bioremediation of legacy lindane-contaminated sites.},
}

@article {pmid42090907,
year = {2026},
author = {Su, X and Li, A and Liu, J and Guo, Y and Yu, H and Yu, J and Wang, R and Garza, DR and Qu, J and Wen, B and Liu, B},
title = {From microbes to molecules: Gut microbiota as a prerequisite threshold determinant for cancer immunotherapy efficacy.},
journal = {Microbiological research},
volume = {309},
number = {},
pages = {128539},
doi = {10.1016/j.micres.2026.128539},
pmid = {42090907},
issn = {1618-0623},
abstract = {Cancer immunotherapy, represented by immune checkpoint inhibitors, adoptive cell therapy, and cancer vaccines, has revolutionized the clinical management of multiple malignant tumors, yet profound interindividual heterogeneity in treatment response and widespread primary/acquired resistance remain the most critical bottlenecks restricting its long-term clinical benefits. Accumulating preclinical and clinical evidence has unequivocally established the gut microbiota as a pivotal regulator of host anti-tumor immune responses. However, the vast majority of existing studies and reviews frame the gut microbiota as a mere adjuvant enhancer of immunotherapy efficacy, focusing solely on its role in boosting the upper limit of treatment effects, while neglecting its more fundamental role as a prerequisite for establishing a responsive immune baseline. In this review, we propose a unifying, evidence-based original core hypothesis: the gut microbiota is not merely an enhancer of cancer immunotherapy efficacy, but an indispensable prerequisite condition that sets the minimal baseline threshold for therapeutic responsiveness-a central thesis that distinguishes this review from previous descriptive work. Guided by this hypothesis, we systematically dissect the taxonomic and functional characteristics of threshold-determining gut microbiota, and clarify that microbial metabolites (e.g., short-chain fatty acids, bile acids, tryptophan derivatives) act as core molecular mediators translating microbial signals into host immune activation, which is critical for establishing the baseline efficacy threshold required for effective immunotherapy. We further perform a critical synthesis of clinical data from prospective cohorts, randomized controlled trials, and microbiota intervention studies, validating that threshold-based microbial signatures serve as non-invasive predictive biomarkers for immunotherapy outcomes, and propose mechanism-driven translational strategies targeting the gut microbiota (e.g., fecal microbiota transplantation, probiotic supplementation, dietary modulation) to reset the impaired immunotherapy efficacy threshold. This review provides a novel theoretical framework for understanding the microbiota-immunotherapy axis, which not only deepens the mechanistic insight into microbial metabolite-mediated immune regulation, but also facilitates the development of microbiota-guided personalized cancer immunotherapy and the overcoming of primary treatment resistance.},
}

@article {pmid42090982,
year = {2026},
author = {Ghanam, AR and Gatermann, S and Juckel, G},
title = {Reduced gut microbiome alpha diversity associates with depressive symptom severity and somatic symptom burden in major depression.},
journal = {Journal of psychiatric research},
volume = {199},
number = {},
pages = {237-242},
doi = {10.1016/j.jpsychires.2026.04.022},
pmid = {42090982},
issn = {1879-1379},
abstract = {OBJECTIVE: Alteration in gut microbiome have been increasingly linked to many psychiatric disorders inclusive depression. However, findings regarding microbiome diversity in depression remain inconsistent. Differences in depression subtypes, particularly the somatic versus affective symptoms profiles may partly explain this heterogeneity in previous results.

METHODS: This cross-sectional study included 31 Participants diagnosed with major depressive disorder. The participants divided into two groups by severity of depression (BDI-II >34 vs. <34) and severity of somatic symptoms of depression (somatic dimension vs. cognitive-affective dimension of BDI-II). Fecal samples were collected, and 16S rRNA gene sequencing of the V3/V4 region was performed on an Illumina platform to profile the gut microbiome. Amplicon Sequence Variants (ASVs) were used to analyze microbial alpha diversity, including ACE, Chao1 and Shannon.

RESULTS: Participants with higher depressive severity showed significantly reduced gut microbiome alpha diversity compared to lower depressive state (ACE; p = 0.019, Chao1; p = 0.019, and Shannon; p = 0.053). Across the total sample, BDI-II total score correlated negatively with alpha diversity significantly for ACE (r = -0.435, p = 0.015), Chao1 (r = -0.435, p = 0.015) and Shannon (r = -0.376, p = 0.037). While the somatic dimension of the BDI-II showed significant negative correlation with all tested alpha diversity indices, no significant correlations were detected between gut microbiome alpha diversity and the cognitive-affective dimension. Shannon diversity further correlated negatively with HDRS-17 scores (p = 0.033).

CONCLUSION: In conclusion, the results show that a lower diversity of gut microbiota alpha is linked to more severe depressive symptoms, specifically the somatic aspect of depression. These results emphasize the importance of considering somatic symptom profiles in microbiome research and point to the gut-brain axis as a potential target for future therapeutic interventions.},
}

@article {pmid42091112,
year = {2026},
author = {Gao, S and Zhao, W and Jiang, J and Guan, X and Pan, Y and Zhao, Z and Wang, B and Xiao, Y and Zhang, G and Zhao, D and Mi, R and Zhou, Z},
title = {Bottom Grinding Increases the Phototrophic Bacteria While Reduces Bacterial Community Stability in Sea Cucumber Cultural Ponds.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70357},
pmid = {42091112},
issn = {1758-2229},
support = {U24A200104//National Natural Science Foundation of China/ ; XLYC2203191//Liaoning Revitalization Talents Program/ ; 2023JH1/10200007//Science and Technology Project of Liaoning Province/ ; 2023RJ007//Dalian Science and Technology Talent Innovation Support Program/ ; 2025HQ1304//undamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; 2025JCX1008//undamental Research Funds of Liaoning Academy of Agricultural Sciences/ ; },
mesh = {*Ponds/microbiology ; Animals ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Microbiota ; *Sea Cucumbers/microbiology/growth & development ; *Aquaculture/methods ; Phototrophic Processes ; Geologic Sediments/microbiology ; Water Microbiology ; },
abstract = {Bottom grinding (BG), which suspends the anaerobic microorganisms deposited at the bottom of the pond through aeration, is a common practice in sea cucumber aquaculture for maintaining water quality. However, little is known about the effects of BG on the environmental microbiome. This study investigated differences in bacterial communities from three niches (surface water, bottom water and sediments) of culture ponds with and without BG operations. Only minor changes in sediment bacterial communities were observed between BG-treated and control ponds. In contrast, the composition of the bacterial communities in the water was also significantly altered by the BG operation, with an increase in Cyanobacteria and a decrease in Proteobacteria. Additionally, functional prediction revealed increased phototrophy and decreased chemoheterotrophy in aquatic bacterial communities following BG treatment. Co-occurrence network analysis revealed that bacterial communities in all three niches were more complex but unstable with BG treatment compared to without, indicating some remedial operations for farming practice. Analysis of community assembly mechanisms showed increased stochastic assembly of bacterial communities in all three niches induced by BG treatment. Overall, this study revealed the effects of BG operation on the bacterial communities in culture ponds, providing insights into the ongoing evolution of farming techniques.},
}

*Ponds/microbiology
Animals
*Bacteria/classification/genetics/isolation & purification/metabolism
*Microbiota
*Sea Cucumbers/microbiology/growth & development
*Aquaculture/methods
Phototrophic Processes
Geologic Sediments/microbiology
Water Microbiology

@article {pmid42091350,
year = {2026},
author = {Monday, L and Krishna, A and Chopra, T},
title = {Prevention and Control of Clostridioides difficile Infection for the Infectious Diseases Clinician.},
journal = {Infectious disease clinics of North America},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.idc.2026.02.009},
pmid = {42091350},
issn = {1557-9824},
abstract = {This article highlights the challenges of preventing Clostridioides difficile infection (CDI) in health care settings. It emphasizes a multifaceted approach including hand hygiene, contact precautions, environmental cleaning, and antimicrobial stewardship. Diagnostic stewardship, using combined testing algorithms and electronic alerts, helps reduce unnecessary testing and misdiagnosis. Emerging strategies like microbiome restoration, vaccines, and monoclonal antibodies are under active investigation. When CDI rates remain high despite standard measures, additional interventions such as sporicidal disinfectants and no-touch technologies may be necessary. Overall, a comprehensive, adaptive approach is essential to effectively reduce CDI incidence and improve patient outcomes.},
}

@article {pmid42091967,
year = {2026},
author = {Vinayagam, S and Bhowmick, IP and Rajendran, D and Arumugam, DK and Sekar, K and Renu, K and Kaur, H and Sattu, K},
title = {Genetic diversity and gut microbiome of Anopheles mosquitoes in Tamil Nadu by using COI DNA barcoding and 16S rRNA metagenomics.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48529-9},
pmid = {42091967},
issn = {2045-2322},
support = {NER/85/2022-ECD-I//ICMR- Adhoc/ ; },
abstract = {Anopheles mosquitoes transmit infections to humans. Identifying the right mosquito species is crucial for vector control evaluation. This study uses COI gene DNA barcoding and 16S rRNA metagenomics to show the genetic diversity and gut microbial profile of undiscovered mosquito species. Three genera were found, including eight morphologically different Anopheles mosquitoes, and six mosquito species were molecularly validated, including An. moghulensis. The analysis of genetic diversity indicated that there is a state of balanced natural selection present. The species An. maculatus s.s. and An. stephensi exhibited nearly identical mutations, while An. moghulensis demonstrated evidence of purifying selection within the studied population. The gut microbiomes of An. moghulensis (149,377 reads), An. maculatus (51,016 reads), and An. dravidicus (33,126 reads) mosquitoes were also revealed. Afipia felis and Prevotella copri were the leading bacterial species, followed by other phyla including Proteobacteriota, Spirochaetes, and Firmicuteota. In An. moghulensis, alpha diversity assessments of Chao I incidence were dominating, whereas Shannon index was plentiful in An. maculatus s.s. mosquitoes. The mosquito's distinct bacterial species and shared microbial community are shown in the Venn diagram. These results suggest that the discovered bacterial taxa might be exploited to create vector control techniques for vector-borne illnesses.},
}

@article {pmid42092044,
year = {2026},
author = {Loukas, A and Kalaentzis, K and Venetsianou, NK and Damianou, C and Paragkamian, S and Lagani, V and Jensen, LJ and Pafilis, E},
title = {CCMRI: a classification and curated database of climate change-related microbiome studies.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-51914-z},
pmid = {42092044},
issn = {2045-2322},
support = {2772//Hellenic Foundation for Research and Innovation/ ; },
abstract = {Climate Change (CC) is reshaping all ecosystem processes and structures. Microbial data provide valuable insights into how microbial processes contribute to CC and how CC, in turn, alters microbial communities. However, the growing volume of environmental genomics data makes identifying CC-related records challenging. The Climate Change Metagenomic Record Index (CCMRI) has been developed to harvest metagenomic/microbiome records pertaining to CC and to provide researchers with a curated database of CC-related microbiome studies (https://ccmri.hcmr.gr). To guide interpretation, the database's 169 metagenomic studies have been labelled according to their relation to CC as CC-caused, CC-causing, and CC-mitigating. They have also been annotated with the CC phenomena they explore, like methane production, temperature rise, permafrost thawing, greenhouse gas emission, methanotrophy, and ocean acidification. To ease navigation, they have also been classified according to their biome as aquatic, terrestrial, host-associated, and engineered. The CCMRI database was initially constructed through manual curation of all aquatic and terrestrial studies in the MGnify resource. It was then expanded with the help of the CCMRI curation-assistant system. This leveraged Large Language Models to scan the remaining MGnify studies, filtered them for relevance, and proposed candidates for inclusion. With a recall greater than 90%, the system achieved high accuracy in identifying CC-related studies. The final decisions on CC-relatedness and categorization were performed by a human curator. This approach combines the efficiency of automation with human oversight and greatly reduces the curation effort, ensuring sustainability and scalability.},
}

@article {pmid42092115,
year = {2026},
author = {Xu, W and Yuan, X and Cao, J and Cui, X and Fu, K and Wang, G and Ling, N and Yin, Y and Shi, Q and Shi, Z},
title = {Trichoderma-based fertilizer enhances quality of Elymus breviaristatus silage via microbial and metabolic modulation.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10028-y},
pmid = {42092115},
issn = {2399-3642},
abstract = {Elymus breviaristatus is an important alpine forage, there is limited information regarding its potential use as silage and how fertilizer treatments affect the ensiling process in this forage crop. Here, we investigated how organic fertilizer (M), nitrogen-phosphorus-potassium fertilizer (NPK), and Trichoderma harzianum fertilizer (B) affect Elymus breviaristatus silage quality (30 days and 60 days ensiling) via microbiome and metabolome analyses. Before ensiling, plant height and chlorophyll content increased by 29.93% and 39.72%, respectively, in the B group. After 60 days of ensiling, the M group had reduced crude protein and elevated butyric acid, the NPK group had higher ammonia nitrogen and butyric acid, and the B group had increased crude protein and lactic acid. These quality shifts correlated with microbial and metabolic changes. In the M group, alpha-linolenic acid metabolism was downregulated and Alternaria enriched, while the NPK group had enhanced flavone biosynthesis and a reduced level of Lactiplantibacillus. The B group had enhanced glycine, serine, and threonine metabolism, and displayed the most complex microbial networks along with increased levels of Lactiplantibacillus and Aspergillus. Overall, these results demonstrate that Trichoderma-based fertilization enhances silage quality by promoting accumulation of beneficial microbes and increasing flux through specific metabolic pathways, potentially offering a sustainable strategy for alpine forage improvement.},
}

@article {pmid42092154,
year = {2026},
author = {Yu, XA and Strachan, CR and Herbold, CW and Lang, M and Gasche, C and Makristathis, A and Segata, N and Pollak, S and Tett, A and Polz, MF},
title = {Genome-wide sweeps create ecological units in the human gut microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42092154},
issn = {1476-4687},
abstract = {The human gut microbiome is shaped by diverse selective forces that originate from host and environmental factors and it substantially influences health and disease. Whereas the association of microbial lineages with various health conditions has been shown at different taxonomic levels[1-5], the extent to which unifying adaptive mechanisms sort microbial lineages into ecologically differentiated populations remains poorly understood. Here we show that genome-wide selective sweeps are a pervasive mechanism that differentiates bacteria in the microbiome. This mechanism leads to population structures akin to global epidemics across geographically and ethnically diverse human populations. Such sweeps arise when an adaptation allows a clone to outcompete others in its niche followed by rediversification, and they manifest as clusters of closely related genomes on long branches in phylogenetic trees. This structure is revealed by excluding recombination events that mask the clonal descent of the genomes. Indeed, we show that genome-wide sweeps originate under a wide range of recombination rates in at least 66 taxa from 25 bacterial families. Estimated ages of divergence suggest that sweep clusters can spread globally within decades and that this process has occurred throughout human history. Sweep clusters are associated with different host conditions-such as age, colorectal cancer, inflammatory bowel diseases and type 2 diabetes-as an indication of their ecological differentiation. Our results reveal an evolutionary mechanism for the observation of stably inherited strains with differential associations and provide a theoretical foundation for analysing adaptation among microbial populations.},
}

@article {pmid42092264,
year = {2026},
author = {Vargas-Robles, D and Santos Agrait, JL and Suárez-Pérez, J and Vázquez, F and Dominicci-Maura, A and Sariol, CA and Zorrilla, C and Romaguera, J and Godoy-Vitorino, F},
title = {Oral Microbiome Resilience During SARS-CoV-2 Infection and Diversity Shifts After COVID-19 Vaccination in a Hispanic Population.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70310},
pmid = {42092264},
issn = {2045-8827},
support = {U54 MD007600/MD/NIMHD NIH HHS/United States ; U54GM133807/GM/NIGMS NIH HHS/United States ; 1P20GM156713-01/GM/NIGMS NIH HHS/United States ; 2U54MD007600/MD/NIMHD NIH HHS/United States ; U54 GM133807/GM/NIGMS NIH HHS/United States ; U01CA260541/CA/NCI NIH HHS/United States ; COVID-19 RAPID GRANT #2020-00269//Puerto Rico Science, Technology and Research Trust/ ; P20 GM103475/GM/NIGMS NIH HHS/United States ; },
mesh = {Humans ; *COVID-19/prevention & control/microbiology/immunology/virology ; *Microbiota ; Hispanic or Latino ; Female ; Male ; SARS-CoV-2 ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Adult ; *Mouth/microbiology ; *COVID-19 Vaccines/administration & dosage/immunology ; Longitudinal Studies ; Vaccination ; Bacteria/classification/genetics/isolation & purification ; Aged ; White ; },
abstract = {The relationship between SARS-CoV-2 infection and the oral microbiome remains poorly understood, particularly in the Hispanic population. Oral samples from 62 individuals (38 SARS-CoV-2 positive, 24 negative) were analyzed using 16S rRNA sequencing, comparing diversity and taxa by infection and symptoms. Longitudinal data from 11 participants assessed microbiome changes as the infection resolved over time. To assess the impact of vaccination, we further examined 68 consistently SARS-CoV-2-negative individuals with paired samples collected before and after vaccination. SARS-CoV-2 infection was not significantly associated with alpha diversity, while beta diversity showed a non-significant but marginal trend (p = 0.051). Prevotella nanceiensis was consistently depleted in infected individuals, even after excluding recent antibiotic users, suggesting a reproducible association with infection status rather than a diagnostic marker. Among infected participants, mucosa-related symptoms were associated with lower Veillonella parvula abundance. Longitudinal data revealed stable microbiome profiles with slightly reduced variance in alpha diversity following viral clearance. In contrast, COVID-19 vaccination in consistently negative individuals was associated with significant increases in Shannon (p = 0.050) and Simpson diversity (p = 0.017), indicating greater evenness without expansion of richness. Beta diversity analyses showed vaccination-related shifts in community composition (PERMANOVA p = 0.026), with increases in Treponema, Campylobacter, Oribacterium, and Selenomonas, and a decrease in Haemophilus. The oral microbiome of Hispanics with mild SARS-CoV-2 infection appeared resilient, with only subtle taxonomic alterations. In contrast, COVID-19 vaccination was associated with short-term increases in diversity and compositional shifts, highlighting its influence on oral microbial ecology.},
}

Humans
*COVID-19/prevention & control/microbiology/immunology/virology
*Microbiota
Hispanic or Latino
Female
Male
SARS-CoV-2
RNA, Ribosomal, 16S/genetics
Middle Aged
Adult
*Mouth/microbiology
*COVID-19 Vaccines/administration & dosage/immunology
Longitudinal Studies
Vaccination
Bacteria/classification/genetics/isolation & purification
Aged
White

@article {pmid42092273,
year = {2026},
author = {Wang, N and Li, X and Wang, L and Zhu, Z and Gu, M and Zou, K and Zhang, J},
title = {Global Trends in Postoperative Sepsis After Pancreatoduodenectomy: A Bibliometric Analysis.},
journal = {The Journal of surgical research},
volume = {323},
number = {},
pages = {48-57},
doi = {10.1016/j.jss.2026.04.010},
pmid = {42092273},
issn = {1095-8673},
abstract = {INTRODUCTION: Postoperative sepsis after pancreatoduodenectomy (PSPD) remains a major determinant of morbidity and mortality. Although extensive clinical studies have explored its risk factors and management, the global research landscape and evolving priorities of PSPD have not been systematically characterized.

METHODS: Publications related to PSPD from 1980 to July 2025 were retrieved from the Web of Science Core Collection. CiteSpace, VOSviewer, and R-based bibliometrix were used to analyze publication trends, collaborative networks, influential journals and references, research hotspots, and emerging trends.

RESULTS: A total of 297 studies were included. Global PSPD research has grown steadily over the past 45 years, with rapid acceleration since 2020. The United States, Japan, Germany, Italy, and China were the leading contributors, supported by high-output institutions such as the University of Verona, Vita-Salute San Raffaele University, and Mayo Clinic. Research hotspots centered on risk stratification, surgical technique optimization, prevention of postoperative pancreatic fistula, and perioperative infection control. Emerging frontiers include surgical site infection prevention, microbiome-gut barrier and bacterial translocation mechanisms, precision risk prediction using machine learning models, and individualized perioperative strategies.

CONCLUSIONS: Global PSPD research has evolved from descriptive clinical studies toward mechanistic, predictive, and precision-oriented investigations. Future progress will likely depend on integrating surgical innovation with microbiological, immunological, and data-driven approaches to enable earlier identification and targeted prevention of PSPD.},
}

@article {pmid42092351,
year = {2026},
author = {Dohlman, AB and Mjelle, R and Wood, HM and Jiang, K and Shumate, A and Lee, I and Piccinno, G and Serna, G and Yakubu, AR and Nuciforo, P and Quirke, P and Huttenhower, C and Segata, N and Meyerson, M},
title = {Biodiversity and biogeography of the multi-kingdom cancer microbiome.},
journal = {Cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cell.2026.04.015},
pmid = {42092351},
issn = {1097-4172},
abstract = {Microorganisms represent an important component of the tumor microenvironment, but conflicting reports have left the extent of microbial prevalence across cancer types unclear, necessitating more robust methods for characterizing tumor-associated microbiomes. We built and benchmarked a host-subtraction and classification pipeline to identify microbiota in whole-genome sequencing data and applied it to 16,369 high-depth tumor whole genomes from the UK 100,000 Genomes Project. After decontamination, microbial signatures were indistinguishable from the background in most cancer types. However, in orodigestive tumors, we detected multi-kingdom polymicrobial communities, including bacteria, fungi, viruses, archaea, and, in some cases, Trichomonas, a protozoan parasite. These communities varied by tumor site and subtype, with increased microbial colonization of microsatellite-instable and polymerase ε (POLE)/polymerase δ (POLD1)-mutated tumors, supported by a correlation between microbial load and tumor mutation burden observed across orodigestive cancers. This analysis helps to resolve pan-cancer microbial structure and links the tumor microbiome to host phenotype and tumor genomic context.},
}

@article {pmid42092466,
year = {2026},
author = {Gavini, CK and Raux, L and Labouèbe, G and Gornick, E and Mc Hugh, S and Elshareif, N and Calcutt, NA and Di Summa, PG and Gorostidi, F and Vonaesch, P and Mansuy-Aubert, V},
title = {A gut-adipose-nerve axis mediates inulin protection against Western diet-induced somatosensory dysfunction.},
journal = {Brain, behavior, and immunity},
volume = {137},
number = {},
pages = {106795},
doi = {10.1016/j.bbi.2026.106795},
pmid = {42092466},
issn = {1090-2139},
abstract = {Westernized diets (WDs)-high in fat and sugar and low in fiber-produce somatosensory deficits, chronic pain, and neuropathy, yet the mechanisms linking diet to peripheral nervous system (PNS) pathology remain incompletely defined. Emerging evidence implicates gut-derived metabolites in sensory homeostasis; for example, fecal microbiota transplantation (FMT) from lean donors to WD fed mice reduces hypersensitivity and attenuates PNS inflammation potentially via modifying short chain fatty acid (SCFA) levels, although FMT outcomes are variable. We therefore tested whether targeted modulation of the gut microbiota with fermentable complex carbohydrates (inulin) producing SCFA could reproducibly improve somatosensory function in WD-fed mice. Using an integrated pipeline-behavioral and physiological assays, peripheral nerve electrophysiology, and molecular and immune profiling-we show that inulin improved thermal and mechanical sensory function indirectly by improving metabolic health and remodeling immune cells in adipose tissue depots. Interestingly, in separate genetic experiments we found that deletion of the SCFA receptor FFAR2 (GPR43) in myeloid cells altered thermal sensitivity and adipose inflammatory gene expression, indicating that immune SCFA sensing can modulate pain-related behavior. These findings identify mechanisms by which dietary fiber indirectly preserves PNS function through effects on adiposity and systemic inflammation and provide a tractable alternative to FMT for mitigating WD-associated sensory neuropathy.},
}

@article {pmid42092549,
year = {2026},
author = {Wester, RJ and Samera, GJ and Walcott, JR and Williams, R and Atkins, G and McCarthy, GC and Baillie, LL and Adams, PJ},
title = {Molecular surveillance of Mycoplasmopsis bovis across dairy farms in Western Canada and 16s microbiome assessment in pneumonic calves.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2026-28245},
pmid = {42092549},
issn = {1525-3198},
abstract = {Mycoplasmopsis bovis (M. bovis) is an important bacterial pathogen that severely impacts the Canadian dairy industry and has been linked to bovine respiratory disease (BRD), a complex that includes pneumonia, as well as mastitis, otitis media, and arthritis. Despite its clinical relevance, limited data exists on its prevalence in Western Canadian dairy herds, and its role within the microbiome in the context of pneumonia remains unclear. This study aimed to determine the prevalence of M. bovis in British Columbia and Alberta and to assess microbial shifts in pneumonic calves to investigate its potential role in BRD. A total of 60 farms were screened for M. bovis using qPCR on bulk tank milk (BTM) and swab samples. M. bovis DNA was detected in 20% of screened farms. However, there were notable differences in detection between swab and BTM samples, highlighting the importance of considering both sample types in surveillance initiatives. Additionally, 82 swab samples from calves in a single herd were analyzed using 16S rRNA sequencing to compare microbial communities across clinical groups. Microbial diversity, differential abundance (ANCOM-BC2), and taxa correlations (SECOM) were assessed. M. bovis presence was not significantly associated with clinical status, although calves with pneumonia exhibited significantly altered microbial diversity compared with healthy calves. M. bovis abundance was significantly enriched, and several commensal taxa were significantly depleted in the pneumonic microbiome. M. bovis abundance was also inversely correlated with some of these taxa, supporting a role in dysbiosis. Overall, these findings suggest that M. bovis is associated with dysbiosis within the respiratory microbiota and may contribute to BRD pathogenesis under conditions of microbial disruption.},
}

@article {pmid42092559,
year = {2026},
author = {Niu, Y and Wang, C and Nie, C and Wu, Y and Huang, R and Zhang, W},
title = {Integrated multi-omics reveals that replacing corn silage with triticale silage improves milk quality via rumen microbiome-metabolome crosstalk in dairy cows.},
journal = {Journal of dairy science},
volume = {},
number = {},
pages = {},
doi = {10.3168/jds.2025-28155},
pmid = {42092559},
issn = {1525-3198},
abstract = {The objective of this study was to evaluate the effects of replacing corn silage with triticale (× Triticosecale Wittmack) silage on lactation performance, milk fatty acid profile, and rumen microbiome-metabolome interactions in dairy cows. In this study, 27 mid-lactation dairy cows were used in replicated 3 × 3 Latin squares with 3 28-d periods and 3 treatments, in which 0, 25, or 50% of the corn silage (DM basis) was replaced with triticale silage. Replacing 25% of corn silage maintained DMI and milk yield, whereas 50% replacement reduced both variables. Diets containing triticale silage lowered SCC and increased the proportion of oleic acid in milk fat. The 50% replacement further increased the proportions of linoleic acid (LA), α-linolenic acid (ALA), and milk protein concentration. In the rumen, the 50% replacement increased pH and NH3-N concentration, and triticale diets increased the proportions of ALA and several C18:1 and C18:2 biohydrogenation intermediates, resulting in a greater UFA proportion and a lower SFA: UFA ratio in rumen fluid. Metataxonomic analysis revealed higher relative abundances of Butyrivibrio_A, Ruminococcus_E, and Prevotella in triticale diets, whereas metabolomic profiling indicated enrichment of pathways related to LA, ALA, and amino acid metabolism. Correlation analysis associated Butyrivibrio_A and Ruminococcus_E with LA oxidation products and amino acid derivatives, indicating the involvement of rumen microbiome-metabolome interactions in shaping the milk UFA responses. Overall, partial replacement of corn silage with triticale silage improved the milk fatty acid profile and udder health indicators without compromising performance at 25% inclusion, indicating that winter triticale is a promising component of forage systems.},
}

@article {pmid42092564,
year = {2026},
author = {Freund, L and Ramirez Leal, B and Hsu, CL},
title = {Impact of alcohol on gut microbial metabolism and the gut-liver-brain axis.},
journal = {Alcohol (Fayetteville, N.Y.)},
volume = {134},
number = {},
pages = {44-53},
doi = {10.1016/j.alcohol.2026.04.009},
pmid = {42092564},
issn = {1873-6823},
abstract = {The gut microbiome includes a large and diverse microbial community that plays a central role in host health, supported by an extensive genomic repertoire that is distinct from and complementary to mammalian enzymatic pathways. Alcohol consumption disrupts this ecosystem, inducing microbial dysbiosis and altering functional interactions between the host and its gut bacteria that can lead to systemic effects. In this review, we examine how alcohol affects gut bacteria, and how these changes impair essential bacterial functions, including short-chain fatty acid production, mucin metabolism, biofilm formation, and bile acid metabolism, that support intestinal, liver, and brain health. We further describe how certain gut bacteria tolerate or produce ethanol, and how these traits contribute to the systemic harms associated with alcohol-induced dysbiosis. Finally, we highlight therapeutic strategies aimed at targeting ethanol-tolerant or ethanol-producing bacteria as potential avenues for preventing or mitigating intestinal inflammation, liver injury, and other metabolic disorders.},
}

@article {pmid42092736,
year = {2026},
author = {Prasad, B},
title = {Predicting Pharmacokinetic Variability and Drug Interaction Risk Using Omics-Based Biomarkers.},
journal = {Clinical and translational science},
volume = {19},
number = {5},
pages = {e70591},
pmid = {42092736},
issn = {1752-8062},
support = {R01 HD081299/HD/NICHD NIH HHS/United States ; //National Institutes of Health (NIH)/ ; },
mesh = {Humans ; Drug Interactions/genetics ; *Biomarkers/analysis ; Pharmacogenetics/methods ; *Pharmacokinetics ; Precision Medicine/methods ; Risk Assessment/methods ; },
abstract = {Interindividual variability in drug pharmacokinetics and susceptibility to drug-drug interactions remain major barriers in precision dosing, particularly for narrow therapeutic index drugs. While genetic factors contribute, much variability arises from dynamic influences such as physiology, disease, age, diet, microbiome, and concomitant medications. Conventional approaches provide limited retrospective insight. Emerging phenotypic biomarkers offer a proactive, mechanism-based strategy to quantify variability, improve exposure prediction, assess drug interaction risk, and individualize dosing beyond pharmacogenomics.},
}

Humans
Drug Interactions/genetics
*Biomarkers/analysis
Pharmacogenetics/methods
*Pharmacokinetics
Precision Medicine/methods
Risk Assessment/methods

@article {pmid42092753,
year = {2026},
author = {Palanisamy, M and Babalola, OO and Ramalingam, S},
title = {Shotgun metagenomic dataset of leaf endophytic microbiome of the garden sage (Salvia officinalis L.).},
journal = {BMC genomic data},
volume = {27},
number = {1},
pages = {},
pmid = {42092753},
issn = {2730-6844},
support = {CMRG2400927//Chief Minister`s Research Grant (CMRG), Government of Tamil Nadu, India/ ; },
mesh = {*Salvia officinalis/microbiology ; *Plant Leaves/microbiology ; *Metagenomics ; *Endophytes/genetics/classification ; *Microbiota ; *Metagenome ; Bacteria/genetics/classification ; Fungi/genetics ; },
abstract = {OBJECTIVES: Garden sage (Salvia officinalis L.) is a traditional medicinal plant known for its rich bioactive secondary metabolites. However, there is limited information about the diversity of endophytic microbial communities, including bacteria, fungi, archaea, and viruses. Therefore, the study employs shotgun metagenomics to generate and make publicly available a dataset representing the leaf endophytic microbiome of Salvia officinalis.

DATA DESCRIPTION: Metagenomic DNA was extracted from leaves of S. officinalis collected as three biological replicates and sequenced using the Illumina NovaSeq X platform. Host-derived and contaminant sequences were removed by mapping reads to the S. officinalis reference genome using BWA-MEM. The resulting high-quality FASTQ files were analyzed to characterize the taxonomic composition of the endophytic microbiome using Kraken2-based classification.},
}

*Salvia officinalis/microbiology
*Plant Leaves/microbiology
*Metagenomics
*Endophytes/genetics/classification
*Microbiota
*Metagenome
Bacteria/genetics/classification
Fungi/genetics

@article {pmid42092798,
year = {2026},
author = {Liu, J and He, S and Zhang, H and Mai, H and Li, X and Liang, H and Cui, P and Lan, L and Liao, W and Huang, Q and Ning, H and Li, Z and Liang, Y and Yang, X and Huang, J},
title = {Machine learning-driven clinical decision support for liver cirrhosis: a gut microbiome-based web prediction model with explainable AI integration.},
journal = {BMC gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12876-026-04890-7},
pmid = {42092798},
issn = {1471-230X},
support = {82160385//National Natural Science Foundation of China/ ; 82273694//National Natural Science Foundation of China/ ; 2024GXNSFBA010104//Natural Science Foundation of Guangxi Zhuang AutonomousRegion/ ; 2023GXNSFDA026036//Natural Science Foundation of Guangxi Zhuang AutonomousRegion/ ; GXJKKJ2025ZC004//Science and Technology Project for Disease Control and Prevention of Guangxi Zhuang Autonomous Region/ ; },
abstract = {BACKGROUND: Liver cirrhosis (LC) is a chronic liver disease with global prevalence. Current diagnostic methods for LC still face limitations in safety and accessibility. We aimed to develop an interpretable machine learning (ML) prediction model for LC using gut microbes and deploy it as a web-based clinical decision support tool.

METHODS: Data were retrieved from PubMed and BioProject databases. Bioinformatics re-analysis and discriminant analysis effect size (LEfSe) analysis was conducted to preliminarily identify key genera associated with LC. Further feature selection was performed using Least Absolute Shrinkage and Selection Operator (LASSO) regression. The independent datasets were combined to form an integrated dataset, which was then subjected to five-fold cross-validation and leave-one-dataset-out (LODO) analysis. Model performance was evaluated using metrics such as the area under the receiver operating characteristic curve (AUC), and the optimal model was selected. The decision mechanism of the optimal model was interpreted using SHapley Additive exPlanations (SHAP), and the model was deployed as a web application using the Streamlit framework.

RESULTS: We ultimately included 11 datasets related to LC. The genera Veillonella, Lachnospira, Romboutsia, Akkermansia, Erysipelatoclostridium, Prevotella, UCG.005, and Streptococcus were identified as key predictors distinguishing LC patients from healthy controls. The Random Forest (RF) model demonstrated the best predictive performance (AUC in five-fold cross-validation: 0.875, 95% CI: 0.823-0.905; AUC in LODO analysis: 0.793, 95% CI: 0.702-0.940) and was deployed as an online LC prediction tool.

CONCLUSION: The interpretable RF model, along with its web-based implementation, has the potential to provide decision support for healthcare professionals and shows promise as a valuable auxiliary tool for LC screening and early clinical intervention.},
}

@article {pmid42093056,
year = {2026},
author = {Itoh, H and Shimoji, H and Nakane, D and Jang, S and Kikuchi, Y},
title = {Soil pH as an external filter shaping stink bug-Burkholderia gut symbiosis.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42093056},
issn = {2049-2618},
support = {19K15724//Japan Society for the Promotion of Science/ ; 22H05065//Japan Society for the Promotion of Science/ ; },
mesh = {Animals ; *Symbiosis ; *Burkholderia/physiology/isolation & purification/genetics/classification ; *Soil/chemistry ; Hydrogen-Ion Concentration ; *Soil Microbiology ; *Gastrointestinal Microbiome ; *Heteroptera/microbiology ; },
abstract = {BACKGROUND: Many animals and plants establish intimate symbiotic relationships with specific microorganisms acquired from the environment. Given the immense diversity of environmental microbiomes, selecting appropriate partners from such a vast microbial pool poses a critical challenge for host organisms. To meet this challenge, hosts have evolved sophisticated internal partner-choice mechanisms that ensure stable associations with beneficial microbes. However, because these symbionts primarily inhabit external environments, environmental conditions themselves are also expected to influence the establishment of symbiosis. Despite this expectation, the mechanistic role of external environmental filters in shaping the intended symbiosis remains largely unexplored. Focusing on stink bugs, which acquire their symbiotic bacteria from soil each generation, we investigated how soil properties influence the establishment of gut symbiosis in terrestrial insects.

RESULTS: Microbiome analyses confirmed that Burkholderia sensu lato overwhelmingly dominates a specific gut organ in six stink bug species from the superfamilies Coreoidea and Lygaeoidea, including serious agricultural pests (relative abundance ranging from 74.5 to 100%). Rearing experiments with isolated Burkholderia revealed that insects were strictly dependent on this symbiont; failure to acquire it from soil severely reduced host growth and reproduction, indicating that the availability of symbionts from soil can represent an ecological constraint. Field surveys identified patches of exceptionally high stink bug density in weedy fields with soil pH < 7.0, whereas such aggregations were absent in fields with pH ≥ 7.0. Laboratory experiments with collected field soils showed that the abundance of Burkholderia in soils was negatively correlated with soil pH, and stink bugs readily acquired their symbionts from soils with pH < 7.0 but rarely from soils with pH ≥ 7.0. Experimental manipulations of soil pH followed by rearing experiments confirmed that increasing soil pH to 7-8 markedly suppressed symbiont acquisition by the host, likely by impairing symbiont growth and motility.

CONCLUSIONS: We demonstrate that, beyond host-intrinsic mechanisms, a soil chemical property can act as an externally filter that constrains symbiont acquisition prior to colonization inside the host in a stink bug-Burkholderia symbiosis. This finding highlights how local environmental conditions can shape the assembly of environmentally acquired insect-microbe symbioses. Video Abstract.},
}

Animals
*Symbiosis
*Burkholderia/physiology/isolation & purification/genetics/classification
*Soil/chemistry
Hydrogen-Ion Concentration
*Soil Microbiology
*Gastrointestinal Microbiome
*Heteroptera/microbiology

@article {pmid42093248,
year = {2026},
author = {Durkin, ES and La Luz Maldonado, A and Keiser, CN},
title = {Exploring microbiome diversity between behavioural strategies in a facultatively parasitic mite.},
journal = {Parasitology},
volume = {},
number = {},
pages = {1-21},
doi = {10.1017/S0031182026102121},
pmid = {42093248},
issn = {1469-8161},
}

@article {pmid42093578,
year = {2026},
author = {Alcamán-Arias, ME and Ramos-Tapia, I and Fuentes, F and Bastías, R and Manzano, CA and Plaza, N and Higuera, G and Araneda, D and Troncoso, M and Ugalde, JA and Vergara, K},
title = {Atmospheric Dispersal and Local Drivers Shape Snow and Air Microbial Communities in the Western Antarctic Peninsula.},
journal = {Environmental microbiology},
volume = {28},
number = {5},
pages = {e70316},
doi = {10.1111/1462-2920.70316},
pmid = {42093578},
issn = {1462-2920},
support = {11200413//ANID/FONDECYT/INACH/ ; 1523A0002//ANID/FONDAP/ ; ATE220061//ANID ANILLO/ ; 1221209//ANID/FONDECYT/ ; },
mesh = {Antarctic Regions ; *Microbiota ; *Snow/microbiology ; RNA, Ribosomal, 16S/genetics ; *Air Microbiology ; *Bacteria/classification/genetics/isolation & purification ; Biodiversity ; },
abstract = {Microbial communities in Antarctica's snow and atmosphere are critical for nutrient cycling and are highly sensitive to environmental change. We characterised the bacterial composition, diversity, and co-occurrence network structure of surface snow and airborne microbiomes from two contrasting bays along the Western Antarctic Peninsula (WAP): Arturo Prat Base (APB; Chile Bay, Greenwich Island) and Yelcho Base (YB; South Bay, Doumer Island), sampled during consecutive austral summers (2022-2023). Surface snow and air samples were analysed using 16S rRNA gene sequencing, diversity indices, and network analyses to evaluate spatial and interannual dynamics. Proteobacteria and Bacteroidota dominated both environments, but community structures differed between sites: APB showed stronger local and anthropogenic signals near logistic stations, whereas YB reflected more stable deposition regimes and distant atmospheric inputs. Airborne communities displayed limited interannual variation and high compositional similarity between sites, consistent with atmospheric seeding by polar air masses. Co-occurrence networks revealed denser, more structured interactions within snow communities, with keystone taxa linking snow and air, sustaining deposition-resuspension dynamics. These findings highlight that long-range atmospheric transport and local conditions shape Antarctic microbial dynamics, providing insights for forecasting microbiome responses and assessing airborne health risks amid human activity and climate change in polar regions.},
}

Antarctic Regions
*Microbiota
*Snow/microbiology
RNA, Ribosomal, 16S/genetics
*Air Microbiology
*Bacteria/classification/genetics/isolation & purification
Biodiversity

@article {pmid42093609,
year = {2026},
author = {Harberts, A and Fondevila, MF and Kreimeyer, H and Miwa, T and Lang, S and Demir, M and Schnabl, B},
title = {Faecal Cathepsin B and S Are Associated With Liver Disease Severity and Adiposity in MASLD.},
journal = {Liver international : official journal of the International Association for the Study of the Liver},
volume = {46},
number = {6},
pages = {e70663},
doi = {10.1111/liv.70663},
pmid = {42093609},
issn = {1478-3231},
support = {R01 AA24726/NH/NIH HHS/United States ; R01 AA031710/NH/NIH HHS/United States ; R37 AA020703/NH/NIH HHS/United States ; P30 DK120515/NH/NIH HHS/United States ; },
mesh = {Humans ; *Cathepsin B/analysis/metabolism ; Female ; Male ; Middle Aged ; *Feces/chemistry ; Gastrointestinal Microbiome ; Severity of Illness Index ; *Adiposity ; Case-Control Studies ; *Cathepsins/analysis/metabolism ; Adult ; *Fatty Liver/metabolism ; Aged ; },
abstract = {BACKGROUND & AIMS: Dysregulation of hepatic cathepsins contributes to metabolic dysfunction-associated steatotic liver disease (MASLD) by promoting inflammation, apoptosis, and fibrosis. However, the role of intestinal cathepsins in MASLD has not been investigated. Given the central role of the gut-liver axis in disease progression, this represents an important knowledge gap.

METHODS: Faecal cathepsin B and S activity was measured in 95 patients with MASLD and 18 healthy controls. Cathepsin activity was correlated with liver disease severity, metabolic parameters, and gut microbiome composition.

RESULTS: Faecal cathepsin B and S activity was higher in patients with MASLD than in healthy controls. Cathepsin B activity was further increased in patients with metabolic dysfunction-associated steatohepatitis. Cathepsin B and S activity correlated with serum transaminases and hepatic steatosis, while cathepsin B activity was additionally associated with liver stiffness. Cathepsin B and S activity correlated with adiposity but showed no associations with other metabolic dysfunction-related parameters. Moreover, gut microbiome composition differed between patients with low vs. high faecal cathepsin B or S activity, respectively.

CONCLUSION: Increased faecal cathepsin B and S activity is associated with liver disease severity and adiposity in MASLD and is linked to alterations of the gut microbiome, suggesting a potential role of intestinal cathepsins in gut-liver axis dysfunction.},
}

Humans
*Cathepsin B/analysis/metabolism
Female
Male
Middle Aged
*Feces/chemistry
Gastrointestinal Microbiome
Severity of Illness Index
*Adiposity
Case-Control Studies
*Cathepsins/analysis/metabolism
Adult
*Fatty Liver/metabolism
Aged

@article {pmid42093690,
year = {2026},
author = {Liao, J and Cui, Y and Wang, Y and Zeng, X and Chen, T and Xiang, Y and Wang, D},
title = {Comparative analysis of the rhizosphere microbiome and transcriptome in clubroot-susceptible and resistant rapeseed (Brassica napus).},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1729220},
pmid = {42093690},
issn = {1664-462X},
abstract = {Clubroot disease, caused by Plasmodiophora brassica, severely threatens the rapeseed industry in China, with an annual affected area exceeding 667000 hectares. To elucidate the mechanisms in clubroot resistance, we compared the differences in soil physicochemical properties, rhizosphere microbiome, and transcriptomic responses between a susceptible variety, HYZ62 (disease index 54.86), and a resistant variety, HYZ5R (disease index 17.05), following P. brassicae infection. The results showed that the electrical conductivity of HYZ5R (R) was 1.73 and 1.57 times that of HYZ62 (S) in the inoculated and uninoculated treatments, respectively. Compared to the 17.18% decrease in alkali-hydrolysable nitrogen content in HYZ62 (S) after inoculation, its content in HYZ5R (R) showed no significant difference. The rhizosphere microbial community significantly differed between HYZ5R (R) and HYZ62 (S), with HYZ5R (R) exhibiting higher relative abundances of several microbial genera, such as Burkholderia-Caballeronia-Paraburkholderia, Humibacter, Dyella, and Trichoderma. Although Bacillus had a significantly higher relative abundance in the rhizosphere of uninoculated HYZ62 (S), its relative abundance decreased by 30.36% after infection. Transcriptome analysis revealed that, compared to HYZ62 (S), the expression of pattern-triggered immunity-related genes, such as CML, WRKY, and PR1, was higher in HYZ5R (R) and was more strongly induced upon inoculation. Effector-triggered immunity-related genes, such as RIN4, RPS5, and HSP90, were consistently expressed at higher levels. In contrast, HYZ62 (S) showed a broad suppression of defense-related gene expression after inoculation. Furthermore, although P. brassicae infection generally suppressed defense-related secondary metabolic pathways, including phenylpropanoid biosynthesis, the expression levels of multiple genes in this pathway remained higher in HYZ5R (R). Together, these results suggest that the higher relative abundances of specific microbial taxa in the rhizosphere and the high expression of defense-related genes are associated with the clubroot resistance in HYZ5R (R).},
}

@article {pmid42093732,
year = {2026},
author = {Shen, Z and Xing, X and Rong, K and Geng, Z and Yang, N and Xu, L and Ge, H and Sang, W},
title = {Short-Term Longitudinal Analysis of Gut Microbiota Dynamics During Anti-CD19 CAR-T Cell Therapy in Diffuse Large B-Cell Lymphoma Patients.},
journal = {Blood and lymphatic cancer : targets and therapy},
volume = {16},
number = {},
pages = {598958},
pmid = {42093732},
issn = {1179-9889},
abstract = {PURPOSE: Alterations in gut microbiota may influence immune response and treatment outcomes in patients with diffuse large B-cell lymphoma (DLBCL). However, the dynamics during anti-CD19 CAR-T cell therapy remain unclear.

METHODS: We conducted a short-term longitudinal microbiome analysis in DLBCL patients (n=12) undergoing CAR-T cell therapy targeting CD19. Stool samples were collected at baseline, 1 week, and 2 weeks post-infusion. 16S rRNA gene sequencing was used to assess microbial diversity, taxonomic composition, and functional pathways. Correlation analyses were then conducted between microbial taxa and inflammatory biomarkers.

RESULTS: Alpha diversity indices showed no statistically significant differences across time points. Beta diversity analysis revealed distinct clustering between baseline and week 1 samples in sPLS-DA, although PERMANOVA did not reach statistical significance. At the phylum level, Bacteroidota abundance significantly increased at week 2 compared with baseline (P = 0.008), accompanied by a marked reduction in the Firmicutes/Bacteroidota ratio. Genus-level heatmap and LEfSe analysis identified enrichment of Parabacteroides, and Prevotella at week 2, whereas baseline samples were enriched in Clostridium sensu stricto 13 and Fusobacterium. Functional prediction indicated that lipoic acid metabolism pathways were significantly upregulated at weeks 1 and 2 compared with baseline (both P < 0.05). Correlation analysis demonstrated that specific bacterial taxa, including Parabacteroides and Prevotella, were positively associated with lymphocyte counts and inversely correlated with C-reactive protein levels.

CONCLUSION: Gut microbiota alterations following CAR-T infusion, characterized by increased Bacteroidota abundance, specific taxonomic shifts, and enhanced lipoic acid metabolism, may provide early microbial signatures for monitoring immune modulation in DLBCL patients.},
}

@article {pmid42093801,
year = {2026},
author = {Busmail, H and Weerakoon, S and Mandefro, BT and Sundara, SV and Lu, X and Avula, S and Mohammed, L},
title = {Fecal Microbiota Transplantation in Inflammatory Bowel Disease: A Systematic Review of Efficacy and Safety.},
journal = {Cureus},
volume = {18},
number = {4},
pages = {e106453},
pmid = {42093801},
issn = {2168-8184},
abstract = {Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammatory condition of the gastrointestinal tract associated with immune dysregulation and alterations in the gut microbiota. Growing evidence suggests that intestinal microbial dysbiosis plays an important role in disease pathogenesis, prompting interest in microbiome-targeted therapies, such as fecal microbiota transplantation (FMT). This systematic review aimed to evaluate the efficacy and safety of FMT in adult patients with IBD. A comprehensive literature search was conducted in PubMed, Embase, Scopus, and the Cochrane Library for studies published between 2020 and 2025 using keywords related to "fecal microbiota transplantation" and "inflammatory bowel disease." Eligible studies included randomized controlled trials (RCTs), cohort studies, systematic reviews, and meta-analyses involving adult patients with UC or CD. Due to clinical and methodological heterogeneity, a structured narrative synthesis was performed in accordance with Synthesis Without Meta-analysis (SWiM) guidelines. Nine studies comprising 1,847 participants met the inclusion criteria, including five RCTs, two systematic reviews, and two meta-analyses. In patients with UC, clinical remission rates ranged from 32% to 40%, with response rates between 44% and 52%. In CD, remission rates ranged from 24% to 31%, although evidence remained limited and heterogeneous. Multi-donor stool preparations and repeated FMT administrations were associated with improved clinical outcomes compared with single-donor protocols or single-dose protocols. Adverse events occurred in approximately 12-15% of patients and were predominantly mild gastrointestinal symptoms, while serious adverse events were rare (<2%). Current evidence suggests that FMT may induce clinical remission in a subset of patients with UC, while evidence in CD remains less consistent. Larger randomized trials with standardized protocols and long-term follow-up are needed to determine optimal donor selection, dosing strategies, and long-term safety.},
}

@article {pmid42093897,
year = {2026},
author = {Zhang, H and Du, Z and Lu, P and Jiang, A and Guo, Y and Liu, Y and Song, Z and Dai, B and Zhang, W},
title = {Intratumoral Microorganisms in Tumors: Current Understanding and Emerging Therapeutic Strategies.},
journal = {MedComm},
volume = {7},
number = {},
pages = {e70754},
pmid = {42093897},
issn = {2688-2663},
abstract = {Recent advances in high-throughput sequencing, spatial omics, and integrative multiomics analyses have established reproducibly detectable microbial communities within tumor tissues, leading to the conceptualization of tumors as complex ecosystems encompassing an "intratumoral microbiota." These microorganisms have increasingly been recognized as contributing to tumorigenesis, progression, and therapeutic response through interactions with the immune system, immunometabolic reprogramming of tissues, chronic inflammation, and genomic instability. Nevertheless, current evidence remains piecemeal and descriptive, with limited systematic consolidation of microbial composition, functional mechanisms, and translation to clinical application, particularly across tumor types and microenvironmental contexts. This review summarizes microbial diversity, tumor-type-specific associations, and multilayered mechanisms including immune modulation, metabolic reprogramming, and signaling rewiring, and discusses emerging applications such as biomarker discovery, prognostic stratification, and microbiome-targeted therapeutics. Special focus is placed on tumor microenvironment, microbiota-derived metabolites, and determinants of immunotherapy responsiveness. Overall, this review underscores the intratumoral microbiota as a dynamic and context-dependent regulatory layer in cancer biology and offers an integrated framework to realize microbiome-informed precision oncology, along with avenues for enhanced patient stratification and personalized therapeutic approaches.},
}

@article {pmid42093997,
year = {2026},
author = {Kuang, J and Zhang, M and Bian, X and Wang, X and Li, X and Wu, Q and Li, J},
title = {Diagnostic and metabolic insights into secondary lactose intolerance in infants via fecal lactose quantification and gut microbiome profiling.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1711945},
pmid = {42093997},
issn = {1664-3224},
mesh = {Humans ; *Lactose Intolerance/diagnosis/metabolism/microbiology ; *Feces/chemistry/microbiology ; *Gastrointestinal Microbiome ; *Lactose/analysis/metabolism ; Infant ; Male ; Female ; Fatty Acids, Volatile/metabolism ; Dysbiosis ; },
abstract = {BACKGROUND: Secondary Lactose intolerance (SLI) is common among infants in China, primarily resulting from secondary lactase deficiency due to mucosal damage. Current diagnostic methods are limited by poor sensitivity and specificity.

OBJECTIVE: To investigate gut microbial composition and metabolic dysfunction in infants with SLI and to explore the potential utility of residual fecal lactose as a non-invasive indicator related to SLI.

RESULTS: SLI infants exhibited significantly higher residual fecal lactose and lactate levels accompanied by reduced fecal short-chain fatty acid (SCFA) availability, consistent with incomplete lactose digestion and altered microbial fermentation. Microbiota profiling revealed marked depletion of Bacteroidetes and certain Firmicutes (e.g. Ruminococcaceae, Erysipelotrichaceae, Peptostreptococcaceae, Megasphaera), along with reduced glycolysis pathways. In vitro fermentation assays demonstrated a consistent reduction in total acid, acetate, and propionate production across multiple media, while lactate and gas production were significantly elevated in SLI samples under lactose, FOS, GOS, and starch-enriched conditions. Butyrate synthesis was partially preserved under protein-rich or minimal carbon media, indicating selective resilience of butyrogenic pathways. Microbial β-diversity analysis confirmed structural dysbiosis, with increased abundance of gas-associated taxa, including Clostridium.

CONCLUSION: Residual fecal lactose, when interpreted alongside microbial and metabolic profiles, may serve as a non-invasive indicator associated with secondary lactose intolerance in infants. These findings delineate microbiota-metabolism features consistent with SLI pathophysiology and provide a conceptual framework for future validation studies and the development of nutritional or probiotic interventions.},
}

Humans
*Lactose Intolerance/diagnosis/metabolism/microbiology
*Feces/chemistry/microbiology
*Gastrointestinal Microbiome
*Lactose/analysis/metabolism
Infant
Male
Female
Fatty Acids, Volatile/metabolism
Dysbiosis

@article {pmid42094015,
year = {2026},
author = {Öz, M and Üstüner, E and Çifci, S},
title = {Medicinal and Aromatic Plant Oils in Aquafeeds: Mechanistic Perspectives on Growth Promotion, Immunomodulation, and Stress Resilience.},
journal = {Aquaculture nutrition},
volume = {2026},
number = {},
pages = {8992384},
pmid = {42094015},
issn = {1365-2095},
abstract = {The aquaculture industry is increasingly transitioning toward sustainable aquafeeds, driven by the economic and environmental necessity to replace marine-derived fishmeal and fish oil with plant- and insect-based alternatives. This nutritional shift introduces physiological challenges, accelerating the search for natural, sustainable functional additives. The primary goal of this review is to comprehensively evaluate the application of medicinal and aromatic plant oils (MAPOs) in aquafeeds, providing mechanistic perspectives on their roles in growth promotion, immunomodulation, and stress resilience. We synthesize current literature to link MAPO chemical composition, particularly phenolic monoterpenes and phenylpropenes, with biological responses, advanced delivery systems, and metabolic pathways. Key findings demonstrate that MAPOs can effectively stimulate appetite, modulate the gut microbiome, and enhance antioxidant defenses via the Nrf2-Keap1 pathway, thereby improving disease resistance. However, a critical limitation in the current literature is the high variability and inconsistent outcomes reported across different aquatic species and developmental stages. These discrepancies are largely attributed to strong chemotypic variability of essential oils, unstandardized extraction protocols, and dose-dependent responses that can sometimes yield neutral or suppressive effects. To successfully transition MAPOs from experimental trials to reliable commercial applications, future research must prioritize standardized dose-response evaluations, address species-specific variability, and utilize advanced formulation technologies such as nanoemulsions.},
}

@article {pmid42094080,
year = {2026},
author = {Park, EM and Makowski, L and Cook, KL},
title = {Editorial: The microbiome in cancer therapy response.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1815455},
pmid = {42094080},
issn = {2813-4338},
}

@article {pmid42094244,
year = {2026},
author = {Hasib, A and Ogada, S and Maina, S and Kuria, S and Peng, MS and Yu, J and Ommeh, SC},
title = {Fecal Microbiota Profiling in Indigenous Backyard and Commercial Chickens Reveals Distinct Taxonomic Signatures.},
journal = {Veterinary medicine international},
volume = {2026},
number = {},
pages = {3146713},
pmid = {42094244},
issn = {2090-8113},
abstract = {Farm management conditions and feeding practices in free-range (backyard), semi-intensive, or intensive production systems significantly influence the poultry gut microbiome, thereby impacting their productive performance and overall health. Here, fecal samples from asymptomatic indigenous backyard chickens raised in a free-range production system, characterized by little to no biosecurity measures in place, and from commercial chickens raised in an intensive production system with enhanced biosecurity measures were subjected to 16S rRNA sequencing analysis. Taxonomic assignment identified 19 bacterial phyla, 137 families, and 238 genera. The most prevalent phyla in indigenous backyard and commercial chickens were Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Spirochaetes. Similarities were detected between bacterial families and genera in both indigenous backyard and commercial chickens; however, the bacterial family Bacillaceae and genus Anoxybacillus were only observed in commercial chickens. Statistical tests performed to evaluate the alpha-diversity and beta-diversity metrics showed no significant difference in the fecal bacterial microbiota of indigenous backyard and commercial chickens, as indicated by the Wilcoxon rank-sum (p = 0.94) and PERMANOVA tests (p = 0.26). This study highlights bacteria that may affect the growth, development, and health of indigenous and commercial poultry raised under various production systems, thereby providing vital insights for the development of effective poultry farm management practices.},
}

@article {pmid42094309,
year = {2026},
author = {Amevor, FK and Uyanga, VA and Velleman, SG and Scanes, CG},
title = {Editorial: Integrated approaches to understanding and improving poultry health, immunity, and productivity: unraveling the role of metabolism.},
journal = {Frontiers in physiology},
volume = {17},
number = {},
pages = {1844387},
pmid = {42094309},
issn = {1664-042X},
}

@article {pmid42094360,
year = {2026},
author = {Yang, R and Severn, M and Aiken, E and Zhou, W and Voigt, A and Walker, G and Koh, A and Gong, M and Thapa, M and Li, S and Milstone, L and Oh, J},
title = {Species and strain diversity in Staphylococcus drive divergent host responses in human skin.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.30.720712},
pmid = {42094360},
issn = {2692-8205},
abstract = {The skin microbiome regulates key skin processes, yet the functional diversity of a dominant genus, Staphylococcus, remains poorly resolved at the strain level for multiple species across its pathogenic and commensal continuum. It is likely that Staphylococcus' effects on skin are diverse at these finest taxonomic resolutions, but current skin models lack the physiological relevance and scalability needed to profile this diversity. Using an organotypic 3D human skin model (reconstructed human epidermis, RHE), we profiled skin responses to 187 Staphylococcus strains across seven dominant species. Canonically 'pathogenic' species (e.g., S. aureus) induced broad inflammatory responses, whereas prototypical 'commensal' species (e.g., S. hominis) elicited more nuanced effects on innate immune and skin barrier responses. Strikingly, S. epidermidis displayed pronounced strain-level heterogeneity, with subsets inducing either 'commensal' or 'pathogen'-like responses despite lacking canonical virulence factors, suggesting pleiotropic effects. Comparative genomics, dual-transcriptomics, untargeted metabolomics, and growth phenotyping revealed species- and strain-specific traits underlying these differential effects on RHE, including the presence of select cell surface proteins and differential arginine metabolism. Together, our study provides the first high-throughput, species- and strain-resolved analysis of skin-Staphylococcus interactions, offering mechanistic insights and a platform for microbiome-based strategies to modulate skin inflammation and diseases.},
}

@article {pmid42094415,
year = {2026},
author = {Wills, LJ and Wang-Heaton, H and Polichnowski, AJ and Thomas, KL and Jewett, BE and Jewett, S and Aldridge, G and Ordway, GA and Brown, RW and Chandley, MJ},
title = {PARP inhibition with 3-aminobenzimide attenuates behavioral, cardiovascular, and neuroinflammatory effects of chronic stress.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.28.721400},
pmid = {42094415},
issn = {2692-8205},
abstract = {BACKGROUND: Major depressive disorder (MDD) affects approximately 20% of the population, with over 30% of cases demonstrating treatment resistance. Postmortem analyses have revealed increased poly (ADP-ribose) polymerase 1 (PARP-1) expression in prefrontal cortical white matter of individuals with MDD, suggesting PARP-1 as a potential therapeutic target. Chronic stress, a major risk factor for depression, affects multiple physiological domains including behavior, cardiovascular function, neuroinflammation, and gut-brain axis signaling.

METHODS: We conducted a comprehensive multi-system investigation of PARP inhibition effects on stress-induced pathophysiology using the social defeat stress/chronic unpredictable stress (SDS+CUS) rodent model. In the primary study, male Sprague-Dawley rats (N=32) underwent 10 days of SDS+CUS while receiving daily treatment with the PARP inhibitor 3-aminobenzamide (3-AB; 40mg/kg), selective serotonin reuptake inhibitor fluoxetine (FLX; 10mg/kg), or saline (0.9% NaCl), with non-stressed controls included. Behavioral outcomes were assessed via sucrose preference and social interaction tests. Neurobiological analyses examined PARP-1 expression, microglial morphology, and proinflammatory cytokine levels (IL-1β, TNF-α, IL-6) in relevant brain regions. In a parallel cardiovascular study, a separate cohort of stressed rats (N=8) received either saline or 3-AB treatment while hemodynamic parameters were monitored via telemetry before, during, and after stress exposure. Exploratory gut microbiome analyses were also conducted (see Supplemental Materials).

RESULTS: Saline-treated stressed rats demonstrated significantly elevated anhedonia and social avoidance compared to all other groups, while 3-AB treatment prevented these behavioral deficits. Cardiovascular monitoring revealed that stressed saline-treated rats developed significant elevations in systolic and mean blood pressure with decreased heart rate compared to baseline, whereas 3-AB treatment prevented these hemodynamic changes. Neurobiological analyses showed that FLX-treated stressed rats unexpectedly exhibited elevated PARP-1 expression in prefrontal cortical gray matter. Microglial morphological analysis revealed significantly more prolate (activated) microglia in the saline-treated stressed rats compared to all other treatment groups. Saline-treated stressed rats exhibited significantly increased hippocampal proinflammatory cytokines, with 3-AB treatment specifically normalizing TNF-α levels.

CONCLUSION: PARP inhibition with 3-AB provides multi-system protection against chronic stress effects, preventing behavioral deficits, cardiovascular dysfunction, and neuroinflammation. These findings establish PARP-1 as a key mediator in the systemic pathophysiology of chronic stress and highlight PARP inhibition as a promising therapeutic approach for stress-related disorders with treatment-resistant features.},
}

@article {pmid42094498,
year = {2026},
author = {Singh, J and Grant, TD and Gulick, AM},
title = {Structure of a Stand-Alone Homodimeric NRPS Condensation Domain Reveals Occlusion of the Canonical Carrier-Protein Interface.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.24.720670},
pmid = {42094498},
issn = {2692-8205},
support = {R01 GM133998/GM/NIGMS NIH HHS/United States ; R35 GM136235/GM/NIGMS NIH HHS/United States ; R35 GM158053/GM/NIGMS NIH HHS/United States ; },
abstract = {Fatty acid amides (FAAs) produced by gut-resident bacteria act as potent modulators of host G protein-coupled receptor signaling, yet the enzymatic mechanisms underlying their biosynthesis remain poorly understood. In many bacteria from the gut microbiome, including Coprococcus eutactus , FAA production is mediated by a nonribosomal peptide synthetase-like pathway that includes OaaC, a free-standing condensation domain that catalyzes amide bond formation between acyl carrier protein (ACP) tethered fatty acids and small-molecule amine acceptors. Here, we combine structural, biophysical, biochemical, and evolutionary analyses to interrogate the molecular basis of OaaC function. Solution scattering and X-ray crystallography reveal that OaaC adopts an atypical homodimeric architecture that occludes the canonical ACP-binding surface and donor access pathways. Mass photometry demonstrates that this homodimer is stable in the absence of substrates and is insensitive to free fatty acids, free amines, and apo-ACP. In contrast, holo or acyl-loaded OaaACP selectively destabilizes the homodimer forming the OaaC-OaaACP complex population. LC-MS reconstitution assays confirm that OaaC catalyzes fatty acid amide formation in vitro and can utilize acyl donors spanning multiple chain lengths and saturation states. Phylogenetic and sequence analyses place FAA-associated condensation domains in a distinct clade most closely related to starter condensation domains and reveal a conserved noncanonical active site motif that differentiates them from PCP-dependent NRPS condensation domains. Together, these findings support a model in which OaaC activity is regulated through substrate-dependent modulation of oligomeric state, providing a model framework for understanding FAA biosynthesis in gut microbes and expanding the known functional diversity of NRPS condensation domains.},
}

@article {pmid42094537,
year = {2026},
author = {Debray, R and Dickson, CC and Webb, SE and Ferretti, P and Meloimet, A and Gilbert, J and Alberts, SC and Blekhman, R and Archie, EA and Tung, J},
title = {Social microbiome transmission predicts microbial specialization and host lifespan in a wild primate.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.29.721577},
pmid = {42094537},
issn = {2692-8205},
abstract = {Social interactions are proposed to provide reliable routes for microbial transmission between animals, facilitating animal-microbiome co-evolution. However, microbiome transmission remains challenging to measure in wild populations. Here we combine behavioral observations of wild baboons with repeated strain-resolved metagenomic profiling to identify individual gut microbial species that follow a dominant mode of social transmission. In an 18-year metagenomic time series from the same population, baboons with higher levels of socially transmitted species lived longer than those with lower levels of socially transmitted species. Socially transmitted species were also more stable and persistent within baboons, yet had narrower host ranges outside of baboons. Thus, social transmission is not only detectable in free-living primates, but may play a special role in both host and microbial fitness.},
}

@article {pmid42094709,
year = {2026},
author = {Mallick, S and Pavloudi, C and Chakkalakkal, GJ and Lažetić, V and Saw, J and Eleftherianos, I},
title = {A dataset on microbiome alterations in Drosophila melanogaster infected by entomopathogenic nematodes.},
journal = {Data in brief},
volume = {66},
number = {},
pages = {112794},
pmid = {42094709},
issn = {2352-3409},
abstract = {The fruit fly Drosophila melanogaster is an excellent model for dissecting the molecular processes that regulate host-microbe interactions and the role of the microbiome in host homeostasis. More recently, the fly has also been used as a model for understanding entomopathogenic nematode infection and host response against these parasites. To gain insights into the effect of entomopathogenic nematode infection on the insect microbiome, D. melanogaster larvae were exposed to Heterorhabditis bacteriophora containing their symbiotic bacteria Photorhabdus luminescens (symbiotic worms) and nematodes lacking their bacterial symbionts (axenic worms). Microbiome changes were examined through 16S rRNA sequencing. Data were collected at 24- and 48-hours following infection of D. melanogaster larvae with either type of nematode. The complete set of raw sequencing data generated in this study has been deposited in the European Nucleotide Archive under accession number PRJEB85826.},
}

@article {pmid42094772,
year = {2026},
author = {Luo, H and Shen, Z and Jian, Y and Wang, M and Luo, S and Wang, J and Nan, L and Tang, L and Rehman, MU and Carbonero, F},
title = {Editorial: Unravelling the wildlife gut microbiome: the crucial role of gut microbiomes in wildlife conservation strategies.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1838495},
pmid = {42094772},
issn = {1664-302X},
}

@article {pmid42094775,
year = {2026},
author = {Nguyen, D and Ovadia, O and Masasa, M and Tarnecki, A and Brennan, NP and Rhody, NR and Main, KL and Guttman, L},
title = {Microbial dynamics along nutrient flow and removal in an integrated multitrophic aquaculture system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1781931},
pmid = {42094775},
issn = {1664-302X},
abstract = {Microbial community assembly in marine integrated multi-trophic aquaculture (IMTA) systems remains poorly understood, particularly across interconnected extractive compartments spanning spatial and temporal scales. Two-step biofilters that incorporate seaweeds and multi-species biofilms (periphyton) are widely used to remove excess nitrogen and phosphorus from aquaculture effluents while simultaneously generating protein-rich, edible biomass. Variations in nutrient composition along these biofilters suggest that microbial diversity and functionality may be differentially shaped within the system. To address this knowledge gap, in this study, using the 16S rRNA gene amplicon sequencing technique, we examined the assembly and potential functions of aquatic microbial communities along the treatment of marine effluent by Ulva fasciata and periphyton, where species selection may occur spatially through microbial colonization of the different plant substrates or through changes in water-nutrient content. At the same time, we assessed temporal dynamics by the weekly changes over 5 weeks. Community structure and functionality demonstrated that environmental heterogeneity primarily determined dissimilarity among microbial communities across the biofilter's compartments. Microbial beta diversity of periphyton, Ulva thallus, and rearing water was distinct over time. This confirmed the important role of environmental selection despite hydraulic homogeneity caused by the high dispersal rate of running water within the interconnected biofilters. The periphyton microbial community harbored the highest alpha diversity, followed by the water microbiome and Ulva-associated microbiota. In terms of functional potential, nitrogen and sulfur metabolism were generally higher in periphyton than in the water and Ulva assemblies. While nitrate reduction by periphyton is associated with the high prevalence of genes involved in denitrification, the Ulva-microbes interaction benefits the alga through bacterial dissimilatory nitrate reduction to ammonia. Overall, these findings provide novel insights into the spatial and temporal dynamics of microbiomes in integrated culture systems, contribute to optimal IMTA designs and microbial management in holistic mariculture.},
}

@article {pmid42095016,
year = {2026},
author = {Li, R and Zhang, S and Liu, Q and Wang, B and Mi, S and Wang, C and Chen, X and He, K and Lv, Y and Gao, X and Fan, Y and Tang, J and Hua, D and Wang, X},
title = {Effects of cotton straw and apple pomace mixed ensilage on growth performance, slaughter performance, meat quality, rumen microbiota and metabolome of Xinjiang Brown cattle.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1796588},
pmid = {42095016},
issn = {2297-1769},
abstract = {This study aimed to investigate the effects of replacing traditional corn silage with cotton straw and apple pomace mixed ensilage feed on the growth performance, slaughter performance, meat quality, rumen microbiota and metabolome of Xinjiang Brown Cattle. Twenty 22-month-old Xinjiang Brown Cattle with similar body conditions were randomly divided into a control group (Con, corn silage) and an experimental group (Tre, cotton straw and apple pomace mixed ensilage). The experiment lasted for 180 days, during which growth performance was evaluated. At the end of the experiment, 6 cattle were randomly selected from each group for slaughter to determine slaughter performance and meat quality. Meanwhile, rumen fluid samples were collected to analyze the rumen microbial community structure using 16S rRNA gene sequencing, and rumen fluid metabolites were analyzed with untargeted metabolomics (LC-MS) technology. The results showed that there were no significant differences in growth performance (average daily gain and final weight) between the two groups. However, compared to the Con group, the carcass weight, dressing percentage and drip loss of the Tre group were significantly decreased (p < 0.05). Rumen fermentation results indicated that the rumen pH value of the Tre group was significantly increased (p < 0.05), while the acetic acid content was significantly decreased (p < 0.05). Microbiome analysis showed that the α-diversity (Shannon and Chao1 indices) of rumen microbiota in the Tre group was significantly higher, and there was a significant difference in β-diversity (p < 0.05); the relative abundance of fiber-degrading bacteria such as Fibrobacter in the Tre group was significantly increased. LC-MS analysis revealed that the contents of beneficial metabolites such as N-Acetyl-L-methionine and Resveratrol were increased in the Tre group. In conclusion, cotton straw and apple pomace mixed ensilage feed can be used as an effective substitute for corn silage, modulating the rumen microbial community structure and altering the metabolite profile, thereby improving meat juiciness. This study provides theoretical support for the resourceful and high-value utilization of agricultural by-products such as cotton straw and fruit pomace in Xinjiang.},
}

@article {pmid42095017,
year = {2026},
author = {An, QT and Li, W and Ren, Y and Liu, X and Yao, L and Li, Y and Zhao, X and Zhang, Y and Feng, P and Du, X},
title = {A comparative study of gut microbiota and metabolites in Tibetan sheep during cold and warm seasons.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1768985},
pmid = {42095017},
issn = {2297-1769},
abstract = {Tibetan sheep, a vital livestock species adapted to the extreme hypoxia, low temperatures, and intense radiation of the Qinghai-Tibet Plateau, rely on gastrointestinal microbiota for ecological balance and host nutrition, metabolism, and immunity. However, the possible associations of gut microbiota and metabolites with seasonal phenology remain unclear. Integrating biochemical, metagenomic, and metabolomic analyses, this study investigated seasonal variations in serum indices, microbial communities, and metabolites to inform enhanced breeding strategies. Analysis of forage nutritional composition showed that warm-season forages had significantly higher concentrations of dry matter (DM), crude protein (CP), and ether extract (EE) (p < 0.01), whereas cold-season forages were characterized by significantly greater levels of neutral detergent fiber (NDF) and acid detergent fiber (ADF) (p < 0.01). Correspondingly, serum analysis revealed significantly higher warm-season concentrations of alanine aminotransferase, total cholesterol, creatinine, and urea nitrogen compared with the cold season (p < 0.01). Gut microbiota composition shifted seasonally, with Bacteroides dominating in warm seasons and Bacillus predominating in cold seasons. Functional metagenomics indicated cold-season enrichment in pathways related to carbon metabolism, ABC transporters, aminoacyl-tRNA biosynthesis, pyruvate metabolism, DNA replication, and methane metabolism (p < 0.01). Metabolomics identified elevated warm-season microbial metabolites (His-Met, leucylleucine, luteolin 7-glucoside, ursolic acid; p < 0.05) and higher cold-season compounds (melatonin, glabrol, prostaglandin E2; p < 0.05), with KEGG enrichment linking these to steroid hormone biosynthesis, fatty acid metabolism, bile acid synthesis, and propanoate pathways. These findings suggest possible associations between seasonal extremes and: (1) modulation of nutrient metabolism (e.g., secondary bile acids and short-chain fatty acids); (2) activation of stress-response pathways (e.g., pentose phosphate pathway, ABC transporters, and DNA replication); and (3) immune regulation mediated by bioactive metabolites. Cold-season enrichment in DNA repair and energy-production pathways may be associated with responses to oxidative stress, whereas warm-season shifts in lipid metabolism are consistent with increased nutrient availability. Fluctuations in key metabolites-such as elevated melatonin in cold seasons and elevated ursolic acid in warm seasons-likely reflect adaptations related to thermoregulation and antioxidant defense. This work provides foundational insights into microbiota-host interactions under extreme environmental conditions, supporting the optimization of supplementation, probiotic use, and sustainable husbandry on the Qinghai-Tibet Plateau.},
}

@article {pmid42095188,
year = {2026},
author = {Li, J and Yang, Y and Wang, Y and Liu, J and Huang, X and Li, Z and Li, J},
title = {Society and the Microbiome: A Biopsychosocial Window Into Comprehensive Well-Being: A Review.},
journal = {Health science reports},
volume = {9},
number = {5},
pages = {e72162},
pmid = {42095188},
issn = {2398-8835},
abstract = {BACKGROUND AND OBJECTIVES: In addition to biological factors, human social behavior, societal structures, and environmental contexts significantly influence the human microbiome. This review examines how socially relevant factors relate to the microbiome to clarify underlying mechanisms and health impacts, aiming to inform effective preventive and therapeutic strategies.

METHODS: We synthesized relevant literature from PubMed using a biopsychosocial framework, integrating structural socio-political and contextual factors to elucidate interactions between social behavior and the microbiota.

RESULTS AND CONCLUSIONS: Social behavior shapes the microbiome through complex biological, psychological, and socio‑cultural pathways, with health consequences involving immune, mental, and metabolic functions. Future research should clarify the fundamental drivers of this relationship, identify individual differences, and employ longitudinal designs to measure sustained effects.},
}

@article {pmid42095223,
year = {2026},
author = {Cheng, Y and Zhang, L and Zhang, M and Yu, J},
title = {Advances in research on the effects of bile acids and their receptors on intestinal function.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1821418},
pmid = {42095223},
issn = {2296-861X},
abstract = {Bile acids (BAs), once regarded primarily as detergents facilitating lipid digestion, are now recognized as pivotal signaling molecules that orchestrate intestinal and systemic physiology through a diverse network of nuclear and membrane receptors, with distinct receptor classes mediating complementary transcriptional and rapid signaling responses, including Farnesoid X Receptor (FXR), Takeda G protein-coupled Receptor 5 (TGR5), Pregnane X Receptor (PXR), Peroxisome Proliferator-Activated Receptor α (PPARα), Vitamin D Receptor (VDR), and Mas-related G protein-coupled Receptor member X4 (MRGPRX4). This review synthesizes recent advances in understanding the molecular architecture of BA signaling, emphasizing receptor structural diversity, spatiotemporal expression patterns along the gastrointestinal tract, ligand specificity shaped by BA chemical modifications, and the emerging roles of microbiota-derived bile acid derivatives and selected non-canonical host targets in intestinal immune and metabolic regulation. Central to this signaling axis is the gut microbiome, which enzymatically reprograms the BAs pool through deconjugation, dehydroxylation, oxidation, and epimerization, as well as emerging reconjugation/amidation pathways, thereby generating classical secondary BAs as well as structurally novel metabolites that modulate host receptor activity and immune-cell programs. In turn, BAs shape microbial composition, establishing a dynamic bidirectional feedback loop critical for maintaining intestinal homeostasis. In addition to classical receptor signaling, selected microbiota-derived BAs metabolites can also influence immune-associated transcriptional regulators, thereby expanding the scope of BAs signaling in mucosal immune homeostasis. Beyond metabolism, BAs-receptor interactions integratively regulate gut barrier integrity via tight junction reinforcement, modulate immune responses through anti-inflammatory pathways and tolerogenic cell induction, and influence gut motility and neuroendocrine signaling. Dysregulation of BAs receptor and metabolite-mediated signaling axes is increasingly implicated in the pathogenesis of inflammatory bowel disease, bile acid malabsorption, diarrhea-predominant irritable bowel syndrome, colorectal cancer-via DNA damage and Wnt/β-catenin pathway activation-and systemic conditions such as obesity, non-alcoholic fatty liver disease, and sepsis-related intestinal injury. Emerging therapeutic strategies aim to restore BAs signaling balance through next-generation receptor modulators, tissue-targeted delivery systems, microbiome-directed interventions, rational use of sequestrants, and synergistic combination therapies, thereby supporting the development of more precise and mechanism-based interventions. Future progress will hinge on interdisciplinary approaches integrating metabolomics, gnotobiotic models, and clinical translation to harness the full therapeutic potential of the BAs signaling network in gastrointestinal and metabolic health.},
}

@article {pmid42095655,
year = {2026},
author = {Weis, AM and Matthews, OJ and Bell, R and Pershing, NL and Dankwardt, A and Fleming, BA and Gigic, B and Schneider, M and Hardikar, S and Toriola, AT and Shibata, D and Li, CI and Byrd, DA and Stephens, WZ and Ulrich, CM and Mulvey, MA and Round, JL},
title = {Isolation of a highly virulent colibactin-positive tumor-promoting strain of Escherichia coli from the gut microbiota of an adult.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0021926},
doi = {10.1128/msphere.00219-26},
pmid = {42095655},
issn = {2379-5042},
abstract = {Recent studies have pointed to critical roles for microbes in both exacerbation of and protection from the development of colon cancer. While much has been learned, the field remains understudied, with functional studies available for only a handful of bacteria. To identify novel microbes associated with colorectal cancer (CRC) development, we employed a preclinical chemical carcinogenesis CRC mouse model using germ-free mice that were colonized with human microbiotas. During the course of these studies, we identified a microbiota that exacerbated CRC, from which we isolated an Escherichia coli strain that had disseminated to the mouse kidneys. This strain, which we designated as AW001, was genetically similar to the reference adherent-invasive E. coli (AIEC) strain NC101 and encoded the DNA-damaging toxin colibactin. In relevant animal models, AW001 worsened both colitis and sepsis, making it a colitogenic AIEC-like strain with the capacity to cause invasive systemic infections similar to extraintestinal pathogenic E. coli (ExPEC). This strain will be a relevant tool to study human-associated intestinal E. coli strains capable of causing disease in mice.IMPORTANCEColorectal cancer (CRC) is a significant burden on human health. A growing body of work has pointed to critical roles for microbes in the exacerbation of and protection from the development of CRC. Specific Escherichia coli strains can produce colibactin, a genotoxin that has been implicated in exacerbating CRC. In this study, we tested human microbiotas in a mouse model of CRC and isolated a colibactin-positive Escherichia coli strain that led to tumorigenesis, disseminated from the gut to the mouse kidneys, caused death, and worsened both colitis and sepsis in murine models. Identification of this strain enhances our collective knowledge and adds an important tool for future studies on the role of microbes and CRC tumorigenesis.},
}

@article {pmid42096014,
year = {2026},
author = {Ng, WS and Ng, NC and Wong, RS and Goh, BH},
title = {Fermented Durian Tempoyak as a Source of Probiotics for Colorectal Cancer Prevention through Gut Microbiome Modulation.},
journal = {Current gastroenterology reports},
volume = {28},
number = {1},
pages = {},
pmid = {42096014},
issn = {1534-312X},
mesh = {Humans ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/prevention & control/microbiology ; *Gastrointestinal Microbiome ; *Fermented Foods/microbiology ; Dysbiosis/complications ; },
abstract = {PURPOSE OF REVIEW: Colorectal cancer (CRC) remains a major global and Malaysian public health concern, with increasing recognition of gut dysbiosis as a contributor to colorectal tumorigenesis. This review examines fermented durian tempoyak as a culturally relevant, probiotic-rich traditional food with potential application in CRC prevention through gut microbiome modulation.

RECENT FINDINGS: Dysbiosis may promote CRC through disruption of gut barrier integrity, chronic mucosal inflammation, immune dysregulation, reactive oxygen species (ROS)-mediated DNA damage, and altered microbial metabolism leading to carcinogenic metabolites such as secondary bile acids and hydrogen sulphide. Tempoyak commonly contains lactic acid bacteria, particularly Lactiplantibacillus plantarum, as well as Limosilactobacillus fermentum and Levilactobacillus brevis. Preclinical evidence suggests that related LAB strains can attenuate NF-κB, MAPK, STAT3, IL-17, and COX-2-associated inflammatory pathways, reduce immune-cell infiltration and oxidative stress, restore mucus and tight junction proteins, modulate bile acid metabolism, and reduce tumor burden in CRC or colitis-associated CRC models. Current evidence supports the mechanistic plausibility of tempoyak-associated LABs as microbiome-based agents for CRC chemoprevention. However, direct evidence using tempoyak-derived strains remains limited, and translation is constrained by strain-specific effects, microbial variability, sensory acceptability, safety and standardisation issues, and uncertain LAB viability after cooking. Future studies should prioritise strain characterisation, starter culture standardisation, probiotic stabilisation strategies, CRC-specific preclinical models, and well-designed human trials in high-risk populations.},
}

Humans
*Probiotics/therapeutic use
*Colorectal Neoplasms/prevention & control/microbiology
*Gastrointestinal Microbiome
*Fermented Foods/microbiology
Dysbiosis/complications

@article {pmid42096024,
year = {2026},
author = {Hu, X and Chen, J and Zhou, Y and Ji, X and Shen, S and Qian, J and Li, T and Xu, F and Zhou, Y and Zhou, D and Zhang, X},
title = {n-3 Polyunsaturated Fatty Acids Improve DSS-Induced Acute Colitis in Mice via Intestinal Barrier Fortification and Gut Microbiome Modulation.},
journal = {Digestive diseases and sciences},
volume = {},
number = {},
pages = {},
pmid = {42096024},
issn = {1573-2568},
support = {82404257//the National Natural Science Foundation of China/ ; 82273621//the National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The increasing global burden of ulcerative colitis (UC) is showing a high incidence in developed countries and a swift rise in developing countries. n-3 polyunsaturated fatty acids (PUFAs), particularly eicosatetraenoic acid (EPA) and docosahexaenoic acid (DHA), have demonstrated anti-inflammatory effects. However, their exact mechanisms in intestinal barrier repair for UC remain incompletely elucidated.

METHODS: Acute UC was induced using 2% dextran sulfate sodium (DSS) and the therapeutic effects of mesalazine, EPA, DHA, and EPA + DHA were evaluated. The mucus barrier was assessed histologically. RT-qPCR and Western blot were used to quantify the expression of Mucin2, mechanical barrier proteins (Claudin-1/Occludin), and key signaling pathways (PI3K/Akt, TNF-α/NF-κB, GPR120/PKA/CREB). Gut microbiome composition was analyzed via 16S rRNA sequencing.

RESULTS: EPA + DHA intervention demonstrated optimal efficacy in alleviating colitis, through establishing an anti-inflammatory colonic lipid microenvironment by elevating the EPA/AA and DHA/AA ratios. Inhibiting PI3K/Akt/NHE3, downregulating TNF-α/NF-κB/DRA, activating GPR120/PKA/CREB/AQP) improved the mucosal barrier and restored tight junction to enhance the mechanical barrier. Furthermore, EPA + DHA significantly increased the abundance of beneficial microbiome like Lachnospiraceae and Ruminococcaceae.

CONCLUSION: EPA + DHA effectively alleviates acute UC in mice by fortifying the colonic mucus-mechanical dual barrier and regulating gut microbiome homeostasis, providing a novel potential strategy for UC adjunctive treatment.},
}

@article {pmid42096120,
year = {2026},
author = {Wu, R and Yao, G},
title = {Research advancement on the correlation between gut microbiota and chronic kidney disease.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42096120},
issn = {1572-9699},
support = {010086//the Beijing Major Epidemic Prevention and Control Key Specialty Intensive Care Medicine Construction Project under Grant/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Renal Insufficiency, Chronic/microbiology/therapy ; Dysbiosis/microbiology ; Probiotics ; Animals ; },
abstract = {Chronic kidney disease (CKD) represents a significant global health challenge, with its progression and complications associated with dysbiosis of the gut microbiota. Patients with CKD demonstrate stage-dependent alterations in the composition of gut microbiota and a reduction in diversity, which is characterized by a decline in beneficial bacteria (e.g., Bifidobacterium, Lactobacillus) and an increase in pathogenic species. This dysbiosis disrupts the gut-kidney axis, resulting in a depletion of protective metabolites such as short-chain fatty acids (SCFAs) and secondary bile acids, while facilitating the accumulation of toxic metabolites including trimethylamine N-oxide (TMAO), indoxyl sulfate (IS), and p-cresyl sulfate (pCS). These toxins contribute to the progression of CKD and cardiovascular complications through mechanisms that involve oxidative stress, inflammation (e.g., NF-ĸB/NLRP3 activation), fibrosis (e.g., TGF-β/Smad signaling), and endothelial dysfunction. Therapeutic strategies aimed at modulating the gut microbiota encompass dietary interventions (such as increasing fiber and plant-based protein), microecological agents (including probiotics and prebiotics), fecal microbiota transplantation (FMT), and adsorbents (e.g., targeting uremic toxins). Although these approaches show promise in delaying CKD progression and alleviating complications, they necessitate further validation through large-scale clinical trials to confirm their efficacy, safety, and the development of personalized protocols. Investigating the gut-kidney axis may provide novel biomarkers and therapeutic opportunities for enhancing CKD outcomes.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Renal Insufficiency, Chronic/microbiology/therapy
Dysbiosis/microbiology
Probiotics
Animals

@article {pmid42096418,
year = {2026},
author = {Santini, AT and Cerqueira, AES and Moran, NA and Resende, HC and Santana, WC and de Paula, SO and da Silva, CC},
title = {Gut microbiota of Brazilian Melipona stingless bees: Dominant members and their localization in different gut regions.},
journal = {PloS one},
volume = {21},
number = {5},
pages = {e0326546},
pmid = {42096418},
issn = {1932-6203},
mesh = {Animals ; Bees/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Brazil ; Symbiosis ; *Bacteria/genetics/classification/isolation & purification ; Phylogeny ; },
abstract = {The gut microbiome of eusocial corbiculate bees, which include honeybees, bumblebees, and stingless bees, consists of anciently associated, host-specific bacteria that play crucial role in nutrition, pathogen defense and host fitness. While the core microbiota of honeybees and bumblebees is well characterized, the composition, spatial organization, and evolutionary dynamics of the microbiota of stingless bees remain poorly understood. This gap is particularly evident in the diverse genus Melipona, where Snodgrassella and Gilliamella, ubiquitous symbionts of honeybees and bumblebees, appear rare or absent, indicating a shift in microbiota composition in these stingless bees. Here, we address this gap by characterizing the microbiota of multiple Melipona species using 16S rRNA amplicon sequencing of newly collected and previously published data from field-collected samples. We also mapped the spatial localization of the dominant microbiota members within the gut regions of Melipona quadrifasciata anthidioides through targeted dissection. The Melipona microbiota is dominated by members of the genera Bifidobacterium, Lactobacillus, Apilactobacillus, Floricoccus, and Bombella, with striking regional structure. Apilactobacillus and Bombella dominate in the crop, whereas Apilactobacillus and other members of the Lactobacillaceae are most abundant in the ventriculus. The ileum lacks Snodgrassella and Gilliamella but contains a putative new symbiont closely related to Floricoccus, as well as strains of Bifidobacterium, Lactobacillaceae (including Apilactobacillus), and Bombella. The rectum is dominated by Bifidobacterium and Lactobacillus. These findings reveal a distinct microbiota architecture in Melipona that differs from other corniculate bees yet retains compartment-specific specialization, suggesting an alternative symbiotic strategy that may reflect unique dietary ecology and evolutionary history. Understanding these patterns advances our knowledge of host-microbe symbiosis and provides a baseline for microbiome conservation in declining stingless bee populations.},
}

Animals
Bees/microbiology
*Gastrointestinal Microbiome/genetics
RNA, Ribosomal, 16S/genetics
Brazil
Symbiosis
*Bacteria/genetics/classification/isolation & purification
Phylogeny

@article {pmid42096491,
year = {2026},
author = {Ma, Z and Shi, H and Bai, X and Wang, Z and Cao, J and Dong, Y and Chen, Y},
title = {Host metabolism shapes the intestinal microbiota: a top-down paradigm of environmental selection pressure.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2667735},
doi = {10.1080/19490976.2026.2667735},
pmid = {42096491},
issn = {1949-0984},
mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Animals ; Dysbiosis/microbiology/metabolism ; Energy Metabolism ; *Host Microbial Interactions ; Intestinal Mucosa/metabolism/microbiology ; Bacteria/metabolism/genetics/classification ; Homeostasis ; },
abstract = {Intestinal homeostasis is not a stochastic microbial assembly but a deterministic outcome orchestrated by host-mediated metabolic gating. Traditional research has prioritized the microbiota's impact on host physiology. However, the consistent expansion of facultative anaerobes, such as Enterobacteriaceae, observed in pathological states like intestinal inflammation, suggests that dysbiosis is fundamentally a consequence of impaired host regulation. Here, we propose a "top-down" paradigm of host metabolic regulation, framing the host as an "ecological engineer" that actively shapes the microbiome through metabolism. We detail three critical metabolic filters: (1) the maintenance of epithelial hypoxia via mitochondrial β-oxidation to suppress aerobic respiration; (2) the implementation of "nutritional immunity" to restrict glucose and inflammation-derived electron acceptors (nitrate and tetrathionate); and (3) the energy-dependent synthesis of the gel-forming mucin 2 (MUC2) mucus layer and antimicrobial peptides (AMPs). We argue that the breakdown of these filters leads to "niche opening," which acts as the fundamental driver of dysbiosis. Finally, we discuss therapeutic strategies aimed at restoring host bioenergetics-including Peroxisome proliferator-activated receptor gamma (PPAR-γ) agonists, melatonin, and ketogenic diets-to rebuild the host's ecological filtration capacity and fundamentally correct dysbiosis.},
}

*Gastrointestinal Microbiome/physiology
Humans
Animals
Dysbiosis/microbiology/metabolism
Energy Metabolism
*Host Microbial Interactions
Intestinal Mucosa/metabolism/microbiology
Bacteria/metabolism/genetics/classification
Homeostasis

@article {pmid42096550,
year = {2026},
author = {Xie, M and Xu, C and Xiang, N and Liao, T and Liu, X and Liu, Z and Feng, X and He, Q and Liang, Z and Wang, W and Dai, Y and Yan, L and Pogoreutz, C and Barra, L and Au, SWN and Jiang, L and Voolstra, CR and Luo, H},
title = {Trait-based signatures associated with persistence and thermal benefit in a genomically decayed coral probiotic.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag106},
pmid = {42096550},
issn = {1751-7370},
abstract = {A key bottleneck in microbiome engineering is ensuring long-term host association of introduced microbes. Selecting probiotic candidates based on evolutionary genomic decay signatures of emerging host dependency offers a potential solution. The Ruegeria strain B4 of population MC10, identified by such signatures, showed persistent coral colonization in a companion study. Whether this persistence translates into measurable host benefit compared to other coral-associated Ruegeria strains, and which mechanisms underlie such benefit, remained unknown. Here we directly compare the probiotic efficacy of MC10-B4 against two sympatric Ruegeria strains isolated from the same coral colony and mucus compartment, controlling for host genotype and microenvironment. MC10-B4 inoculation significantly increased heat stress tolerance in the model cnidarian Aiptasia (Exaiptasia diaphana strain H2), outperforming both controls. To understand the mechanistic basis, we characterized the functional profile of MC10-B4 using integrated multi-omics. The MC10 genome is enriched in host-interaction genes, including siderophore-mediated iron acquisition and exopolysaccharide biosynthesis, confirmed phenotypically by iron scavenging and enhanced biofilm formation. Following exposure to coral tissue extract, MC10-B4 underwent a coordinated "motile-to-sessile" proteomic reprogramming, downregulating flagellar motor components whereas upregulating flagellin and biofilm regulators. This response was distinct from sympatric relatives, which instead mounted broad upregulation of nutrient acquisition systems. MC10-B4's functional profile, particularly its oxidative stress sensitivity, contrasts with traits favored in conventional probiotic screens. Our results provide mechanistic insight into traits associated with long-term host association and thermal benefit, validating an evolution-guided approach that prioritizes innate colonization potential over pre-defined laboratory functionalities for rational probiotic design.},
}

@article {pmid42096749,
year = {2026},
author = {Kafkoutsou, AL and Stewart, M and Bakali, U and Beaver, CC and O'Connor, G and Kobetz, EN and Caban-Martinez, AJ and Deo, SK and Daunert, S and Schaefer Solle, N},
title = {Vaginal polycyclic aromatic hydrocarbons (PAHs), HPV infection, and vaginal microbiome in firefighters: A cross-sectional study.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142072},
doi = {10.1016/j.jhazmat.2026.142072},
pmid = {42096749},
issn = {1873-3336},
abstract = {Female firefighters are routinely exposed to combustion-derived toxicants, yet the reproductive health implications of this exposure are largely unknown. We investigated whether polycyclic aromatic hydrocarbons (PAHs) are detectable in the vaginal tract of female firefighters and whether these contaminants are linked to high-risk human papillomavirus (HPV) infection and vaginal microbiome alterations. In this cross-sectional study 49 female firefighters and 51 community controls self-collected vaginal swabs for analysis of 16 EPA-priority PAHs, high-risk HPV, and microbial composition. All 16 PAHs were detectable and median total PAHs were 3-fold higher in firefighters than controls (p < .0001). PAH burden increased with firefighting tenure showing a strong positive correlation between high- and low-molecular-weight congeners (r = 0.85). High-risk HPV was detected in 12.2% of firefighters versus 3.9% of controls and was associated with higher PAH levels (p = 0.02). Firefighters exhibited a microbiome shift characterized by increased relative abundance of Gardnerella (r = 0.32 with total PAHs) and reduced Lactobacillus dominance. Detection of vaginal PAHs along with their associations with HPV and dysbiosis, suggests a previously unrecognized pathway by which occupational exposures may elevate cervical cancer risk. Targeted exposure reduction policies and vigilant gynecologic screening should be considered for this underserved workforce.},
}

@article {pmid42096978,
year = {2026},
author = {Crespo-García, C and Taaffe, DR and Peddle-McIntyre, CJ and Jeffery, E and Campbell, JP and Thomas, R and Galvao, DA and Newton, RU},
title = {Precision nutrition in breast cancer: Towards patient- and tumour-informed dietary strategies.},
journal = {Clinical nutrition (Edinburgh, Scotland)},
volume = {61},
number = {},
pages = {106670},
doi = {10.1016/j.clnu.2026.106670},
pmid = {42096978},
issn = {1532-1983},
abstract = {Dietary strategies are increasingly recognized as important modulators of breast cancer outcomes, acting through effects on metabolic regulation, weight management, hormone signalling, immune function, and the gut microbiome. However, breast cancer heterogeneity and inter-individual variability mean that generic dietary guidelines may not fully capture patient needs. Precision nutrition offers the opportunity to align dietary interventions with tumour subtype, treatment context, and host biology, potentially enhancing therapeutic response and survivorship in patients diagnosed with breast cancer. In this narrative review, we summarize evidence on dietary patterns and prognosis, and explore how targeted interventions, including fasting regimens, ketogenic diets, and caloric restriction, may be informed by and targeted to host factors such as obesity, metabolic dysfunction, genetics and epigenetics, and microbiome composition, as well as tumour and treatment characteristics. We also discuss the emerging role of digital tools and multi-omics approaches to support personalization. While clinical translation is at an early stage, refining dietary recommendations through precision approaches may open new opportunities to improve prognosis and long-term care in breast cancer.},
}

@article {pmid42097107,
year = {2026},
author = {Panyakhamlerd, K and Rungruxsirivorn, T and Panichaya, P and Nimitpanya, P and Payungporn, S and Ariyasriwatana, C and Suwan, A and Visedthorn, S and Ruengket, P and Tanprasertkul, C},
title = {The effect of hormone therapy on vaginal microbiota in women with genitourinary syndrome of menopause: A double-blind, randomized, placebo-controlled trial.},
journal = {Maturitas},
volume = {209},
number = {},
pages = {108963},
doi = {10.1016/j.maturitas.2026.108963},
pmid = {42097107},
issn = {1873-4111},
abstract = {This double-blind, randomized, placebo-controlled trial investigated the effects of oral combined menopausal hormone therapy (MHT) on vaginal microbiota and clinical outcomes in postmenopausal women with genitourinary syndrome of menopause (GSM). Thirty-four healthy postmenopausal women aged 40-60 years with moderate to severe GSM were randomized to receive either oral estradiol 1 mg/dydrogesterone 5 mg (Femoston conti®) or placebo daily for 12 weeks. Vaginal microbiota was assessed at baseline and week 12 using 16S rDNA gene sequencing. Clinical outcomes, including the most bothersome symptom (MBS), vaginal atrophy score (VAS), vaginal pH, vaginal health index (VHI) and vaginal maturation value (VMV), were evaluated at baseline, week 6, and week 12. The MHT group demonstrated significant more improvement in all clinical measures compared with placebo: MBS (p = 0.008), VAS (p < 0.001), vaginal pH (p = 0.001), VHI (p < 0.001) and VMV (p < 0.001). However, no significant differences were observed in microbial composition or diversity between groups after treatment. These findings suggest that while systemic hormone therapy provides meaningful symptom relief and improves vaginal tissue health, these clinical benefits can occur without concurrent, statistically significant changes in the vaginal microbiota. This supports the clinical value of early systemic MHT in managing GSM, even in the absence of microbiome restoration.},
}

@article {pmid42097142,
year = {2026},
author = {El Mouali, Y and Tawk, C and Huang, KD and Sivapornnukul, P and Mengoni, C and Segata, N and Strowig, T},
title = {Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.006},
pmid = {42097142},
issn = {1934-6069},
abstract = {In the human gut, oxygen levels decrease with increasing distance from the epithelium, creating a gradient that dictates the spatial distribution of commensal bacteria based on varying oxygen tolerance. However, dietary and lifestyle changes can disrupt this ecosystem. Segatella copri, a prevalent ancestral commensal, typically displays greater oxygen sensitivity than Bacteroides species. Here, we find that the transcriptional regulator PerR controls a genetic network underlying S. copri's oxygen response that is critical for gut colonization. Notably, a subset of S. copri strains have acquired an additional oxygen response regulator, OxyR, likely through horizontal gene transfer from other Bacteroidales, conferring enhanced oxygen tolerance. Interestingly, OxyR-positive strains are more prevalent in industrialized countries yet absent in contemporary humans with traditional lifestyles and in ancient human samples. These findings point to recent evolutionary pressures on Segatella, potentially driven by lifestyle changes, which may impact the spatial distribution of the human gut microbiome.},
}

@article {pmid42097143,
year = {2026},
author = {Antunes Fernandes, K and Sanders, F and Cafiero, TR and Huang, C and Reyes, J and Biswas, A and Lim, AI},
title = {Maternal helminths rewire the microbiota to promote offspring antiviral immunity.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.04.009},
pmid = {42097143},
issn = {1934-6069},
abstract = {Maternal environmental exposures can alter microbiome composition and lead to changes in offspring immunity. Industrialization has led to significant shifts in the microbiome, but whether these have transgenerational impacts remains unclear. Here, we discovered that maternal helminths, an evolutionarily conserved mammalian partner lost in industrialized societies, confer broad and lasting protection against respiratory viruses in offspring. This heterologous antiviral immunity is mediated by helminth-induced changes in the maternal microbiota. The tryptophan metabolite indole-3-propionic acid (IPA), derived from helminth-altered microbiota, induces lung epithelial IFN-I responses and is sufficient to protect offspring from respiratory syncytial virus (RSV) and influenza A virus infections. Analysis of chronically helminth-infected human populations reveals gut microbiota enriched for tryptophan metabolic capacity. Additionally, IPA treatment is sufficient to enhance antiviral IFN-I signaling in human bronchial epithelial cells. Collectively, this work uncovers the importance of maternal helminth-driven trans-kingdom crosstalk across generations and highlights microbial metabolites as actionable strategies to strengthen antiviral defense.},
}

@article {pmid42097354,
year = {2026},
author = {Kaliappa, GD and Palanisamy, H and Vidyalakshmi, S},
title = {Integrative Machine Learning Models to Unravel Gut Microbial Dysbiosis and Functional Disruption in Polycystic Ovary Syndrome.},
journal = {F&S science},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.xfss.2026.04.005},
pmid = {42097354},
issn = {2666-335X},
abstract = {OBJECTIVE: To study gut microbial diversity and metabolic pathway disruptions in women with PolyCystic Ovary Syndrome (PCOS) compared to healthy controls, and to evaluate the diagnostic potential of microbiome-driven machine learning models.

DESIGN: Case-controlled metagenomic data analysis SUBJECTS: Gut metagenomic data from women diagnosed with PCOS and age-matched healthy female controls EXPOSURE: Presence of PolyCystic Ovary Syndrome (PCOS) MAIN OUTCOME MEASURES: The primary outcome measures will include gut microbial alpha and beta diversity indices, microbial taxon abundance, functional pathway profiles, predicted metabolite levels, microbe-functional pathway-metabolite interaction networks, and the diagnostic accuracy of microbiome-based machine learning models.

RESULTS: Alpha and beta diversity analyses revealed marked gut microbial dysbiosis in women with PCOS, despite comparable species richness to healthy controls. Differential abundance analysis identified 41 significantly altered microbial species, including enrichment of pro-inflammatory taxa such as Bacteroides vulgatus and Ruminococcus gnavus, and depletion of beneficial commensals including Roseburia hominis and Prevotella copri. These compositional shifts indicate a pro-inflammatory microbial community structure in PCOS. Functional profiling demonstrated the upregulation of pathways involved in nucleotide turnover, lipid and carbohydrate metabolism, and neurotransmitter synthesis, potentially contributing to metabolic and neuroendocrine disruption. Network analysis revealed fragmented and unstable microbial-metabolite associations in PCOS compared with cohesive networks in controls. Microbiome based machine learning models achieved a diagnostic accuracy of 84.25% (AUC 0.93), underscoring their predictive potential.

CONCLUSION: The gut microbiome in PCOS is characterized by a pro-inflammatory community structure and disrupted metabolic pathways. These findings demonstrate the diagnostic potential of microbiome-based models and underscore the gut microbiome as a promising target for therapeutic interventions in the management of PCOS.},
}

@article {pmid42097383,
year = {2026},
author = {Yang, Z and Liang, Z and Cao, L and Li, S and Gao, L and Tian, D and Qiu, Z and Chen, J},
title = {Altitude-Dependent Variations in Environmental Conditions and Human Activities Regulate Microbial Community Assembly and Carbon Metabolism Patterns in Headwater Rivers.},
journal = {Environmental research},
volume = {},
number = {},
pages = {124656},
doi = {10.1016/j.envres.2026.124656},
pmid = {42097383},
issn = {1096-0953},
abstract = {Microorganisms are core drivers of biogeochemical processes in headwater stream ecosystems, yet the response mechanisms of their community composition and carbon metabolic traits to altitudinal gradients and local environmental conditions remain poorly resolved. Elucidating these altitude-dependent patterns is critical for understanding microbiome-mediated ecosystem functioning in vulnerable headwater freshwater habitats. Here, we investigated microbial community structure and carbon substrate utilization in three headwater streams with >1000 m altitudinal span, combining 16S rRNA gene amplicon sequencing, Biolog EcoPlate metabolic phenotyping, and multivariate statistics to characterize microbial taxonomic and functional diversity and their key environmental drivers. Proteobacteria (45.7% average relative abundance) and Bacteroidota (13.6%) dominated all samples, collectively accounting for >60% of the total community. A 1000 m altitude was identified as the ecological threshold, with significant divergences in microbial diversity, community assembly, and carbon utilization patterns across this boundary. Stochastic processes dominated community assembly in steep-gradient streams (68% relative contribution), while deterministic homogeneous selection prevailed in topographically gentle streams (67% contribution); increasing human activity shifted the dominant assembly process from homogeneous selection (67%) to heterogeneous dispersal (52%). Microbial carbon utilization efficiency showed three distinct altitudinal patterns (decreasing, hump-shaped, U-shaped). Variation partitioning analysis revealed that altitude, hydrochemistry, and water physical parameters independently explained 21%, 17%, and 9% of community variation, respectively. Proteobacteria acts as the key phylum governing carbon utilization. This study confirms that altitude is a pivotal driver of headwater microbial diversity and metabolic function, and microbes can adapt to environmental changes by adjusting carbon substrate utilization strategies. Our findings provide new insights into the links between microbial functional traits, ecosystem stability, and nutrient cycling in headwater streams.},
}

@article {pmid42097542,
year = {2026},
author = {Habibyan, YB and Sharkey, KA and Nasser, Y},
title = {PROTEASES AND ABDOMINAL PAIN - OLD DOG, NEW (MICROBIAL) TRICKS.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101803},
doi = {10.1016/j.jcmgh.2026.101803},
pmid = {42097542},
issn = {2352-345X},
}

@article {pmid42097543,
year = {2026},
author = {Peisl, S and Melum, E},
title = {From Kimchi to PSC: Leuconostoc citreum LB-P8 as a microbiome-based therapeutic approach.},
journal = {Cellular and molecular gastroenterology and hepatology},
volume = {},
number = {},
pages = {101800},
doi = {10.1016/j.jcmgh.2026.101800},
pmid = {42097543},
issn = {2352-345X},
}

@article {pmid42097977,
year = {2026},
author = {Krifors, A and Larsson, T and Wångdahl, A and Stensvold, CR},
title = {Time to rethink Blastocystis in faecal microbiota transplantation.},
journal = {Trends in parasitology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pt.2026.04.005},
pmid = {42097977},
issn = {1471-5007},
abstract = {Blastocystis commonly colonises the human gut, but its presence has traditionally led to the exclusion of faecal microbiota transplantation donors. Emerging evidence links it to greater microbial diversity and favourable metabolic profiles, while no harm is seen in immunocompetent recipients. Routine screening may be unnecessary, except for subtype-specific testing in immunocompromised patients.},
}

@article {pmid42098022,
year = {2026},
author = {Baba, Y},
title = {[Esophageal Cancer and Gut Microbiome].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {53},
number = {3},
pages = {158-161},
pmid = {42098022},
issn = {0385-0684},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Esophageal Neoplasms/microbiology/therapy ; },
abstract = {The gut microbiota has recently garnered considerable attention across the medical field, as its involvement has been reported in a broad spectrum of conditions including cancer, obesity, inflammatory bowel disease, and even neuropsychiatric disorders. The human body is composed of approximately 30 trillion human cells and an almost equal number of bacterial cells, forming a highly integrated symbiotic relationship. While the human genome encodes only about 20,000 genes, the gut microbiota harbors several million to tens of millions of genes, offering an overwhelmingly greater genetic repertoire. The composition of the microbiota is influenced by diet, lifestyle, medications, and aging, thereby shaping unique individual - specific patterns. Regional and temporal variations are also recognized, and functional redundancy among different bacterial taxa, known as"functional mimicry,"further underscores its flexibility. Thus, the gut microbiota should be regarded as a dynamic and modifiable ecosystem rather than a fixed entity, making it a promising target for disease prevention and therapeutic intervention. In the context of esophageal cancer, emerging evidence indicates that alterations in the microbiota may affect carcinogenesis, disease progression, and therapeutic responses. These insights highlight the potential of the microbiota as both a biomarker and a therapeutic target, and suggest that integrating microbiome research into clinical oncology could open new avenues for improving patient outcomes.},
}

Humans
*Gastrointestinal Microbiome
*Esophageal Neoplasms/microbiology/therapy

@article {pmid42098023,
year = {2026},
author = {Shibata, T},
title = {[Microbiome and Colorectal Cancer].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {53},
number = {3},
pages = {162-167},
pmid = {42098023},
issn = {0385-0684},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/genetics ; *Microbiota ; Mutation ; Peptides ; Polyketides ; },
abstract = {The number of colorectal cancer patients in Japan continues to rise, placing the country among the highest rates globally, surpassing even Western nations. Furthermore, the increase in colorectal cancer among younger individuals(under 50 years old)is a significant concern. This rapid rise in colorectal cancer patients cannot be explained solely by the adoption of Western lifestyles, suggesting the presence of unknown carcinogenic factors. Colibactin toxin, produced by certain gut bacteria (pks+ Escherichia coli), binds to AT-rich DNA and induces characteristic mutation patterns. An international collaborative study compared the differences in these mutation patterns across 981 colorectal cancer samples collected from 11 countries, including Japan. Surprisingly, it revealed that Japanese cases exhibited a significantly higher frequency of the colibactin toxin - induced mutation patterns(SBS88 and ID18)compared to other countries. Furthermore, SBS88 and ID18 were particularly prevalent in younger patients and notably prominent in the right colon, including the rectum. These findings suggest that interventions such as preventing infection with pks+ bacteria, eradicating them, or inhibiting the function of colibactin toxin could potentially reduce the incidence of colorectal cancer, particularly in younger patients. Such prevention is also considered likely to be effective in Japan, where infection is presumed to be highly prevalent.},
}

Humans
*Colorectal Neoplasms/microbiology/genetics
*Microbiota
Mutation
Peptides
Polyketides

@article {pmid42098024,
year = {2026},
author = {Oya, Y and Tanaka, I},
title = {[Current Status and Future Perspectives of Microbiome Research in Lung Cancer].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {53},
number = {3},
pages = {168-174},
pmid = {42098024},
issn = {0385-0684},
mesh = {Humans ; *Lung Neoplasms/microbiology/drug therapy/immunology/therapy ; *Microbiota ; *Gastrointestinal Microbiome ; },
abstract = {Recent advances in immune checkpoint inhibitors(ICIs)and molecular targeted therapies have substantially improved outcomes in lung cancer; however, marked inter-individual variability in efficacy and toxicity remains. Accumulating evidence suggests that the gut microbiota, acting through the"gut-lung axis,"is a key modifier of treatment response and tolerance in this setting. High microbial diversity and the abundance of beneficial taxa such as Akkermansia, Bifidobacterium, and Faecalibacterium have been associated with favorable ICI responses, whereas dysbiosis induced by antibiotics, proton pump inhibitors, cytotoxic chemotherapy, or lifestyle factors is linked to reduced efficacy and increased toxicity. Microbial metabolites, including short-chain fatty acids and tryptophan derivatives, shape antitumor immunity by modulating T-cell activation, regulatory T-cell differentiation, and the tumor immune microenvironment. In addition, emerging data indicate that the gut microbiota may influence the pharmacodynamics and adverse event profiles of EGFR tyrosine kinase inhibitors(EGFR- TKIs)and other targeted agents, particularly with respect to gastrointestinal toxicity. Smoking, a central etiological factor in lung carcinogenesis, also alters gut microbial composition, decreasing beneficial anti-inflammatory species and promoting pro-inflammatory taxa, thereby potentially aggravating systemic inflammation and impairing ICI responsiveness. Notably, partial restoration of a healthier microbiome appears possible with smoking cessation and rational supportive care. Interventions aimed at favorably modifying the gut ecosystem-such as high-fiber or plant-forward diets, probiotics, and fecal microbiotatransplantation-have begun to show promise in enhancing ICI efficacy without substantially increasing immune-related adverse events. Prospective trials in lung cancer are now underway to evaluate the clinical utility of microbiome-based biomarkers and interventions. Collectively, these findings position the gut microbiota as both a predictive biomarker and a modifiable therapeutic target, with the potential to refine patient stratification, optimize treatment selection, and advance truly personalized medicine in lung cancer.},
}

Humans
*Lung Neoplasms/microbiology/drug therapy/immunology/therapy
*Microbiota
*Gastrointestinal Microbiome

@article {pmid42098025,
year = {2026},
author = {Fukushima, H and Ishikawa, D and Nagahara, A},
title = {[Gut Microbiota Transplantation for Esophageal and Gastric Cancer].},
journal = {Gan to kagaku ryoho. Cancer & chemotherapy},
volume = {53},
number = {3},
pages = {175-181},
pmid = {42098025},
issn = {0385-0684},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/therapy/microbiology/immunology ; *Esophageal Neoplasms/therapy/microbiology/immunology ; *Fecal Microbiota Transplantation ; },
abstract = {Immune checkpoint inhibitors(ICIs)have remarkably improved survival with durable response for patients with multiple cancer type. But, the accurate predictors of response and toxicity to immunotherapy are still unclear. In recent years, the human microbiota, specially the gut microbiota, has been attracting attention in various fields, and it is one of the topics in the field of oncology. The gut microbiome, which refers to the microorganisms and their genes, affects the host immunity both locally and systemically. Modulation of the gut microbiota alters the immune systems and affects the efficacy of ICI. Many clinical trials targeting the gut microbiota, such as fecal microbiota transplantation(FMT)and biotics intervention, are currently being conducted. In this review, we consider the evidence on the role of the microbiome in cancer patients and research began the impact of FMT on the efficacy of ICIs in cancer. ln the future, research on carcinogenesis mechanisms and advance cancer treatment focusing on the human microbiota will become in creakingly active.},
}

Humans
*Gastrointestinal Microbiome
*Stomach Neoplasms/therapy/microbiology/immunology
*Esophageal Neoplasms/therapy/microbiology/immunology
*Fecal Microbiota Transplantation

@article {pmid42098165,
year = {2026},
author = {Sharma, MK and Agarwal, N and Stadulis, SE and Dugan, EM and Giovannoni, CB and Glesener, H and Abdollahzadeh, D and Tanveer, H and Gracey, PR and Huang, M and Gibney, PA and Voth-Gaeddert, LE and Tako, E},
title = {Dietary grape pomace mitigates high-NSP-induced inflammation and production loss via microbiome-SCFA-immune mediated pathways.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00996-8},
pmid = {42098165},
issn = {2055-5008},
abstract = {The United States poultry industry is transitioning away from antibiotic growth promoters (AGP) to antibiotic-free programs, which may increase the risk of chronic intestinal inflammation due to exposure to multiple factors. Grape pomace (GP), a polyphenol-rich by-product, might be a promising candidate for mitigating such inflammation. This study investigated the fermented and non-fermented GP as potential substitutes for antibiotic growth promoters in broilers. A total of 126 broilers were divided into six treatment groups: (i) standard diet (STD), (ii) high non-starch polysaccharide diet (NSP), (iii) NSP + zinc bacitracin (AGP), (iv) NSP + 0.5% GP (GP), (v) NSP + 0.5% Lactobacillus casei fermented GP (LAB FGP), and (vi) NSP + 0.5% Saccharomyces cerevisiae fermented GP (YST FGP). NSP-fed birds exhibited reduced growth and increased TNF-α and IL-1β expression, indicating chronic inflammation. GP and FGP suppressed cytokine expression, modulated microbial homeostasis, and increased butyrate production, suggesting functional modulation of the cecal microbiome. Exploratory correlation identified the Lactobacillaceae-butyrate-IL-1β pathway, positively associated with growth, microbiome, and SCFA production, and negatively associated with inflammation. Overall, incorporating 0.5% of GP or FGP into the diet may serve as an effective alternative to AGPs in broiler production, with the added benefits of antioxidants and prebiotics.},
}

@article {pmid42098175,
year = {2026},
author = {Niu, Z and Xu, J and Hou, X and Liu, G and Yao, J and Cao, Y and Du, Q and Tong, D and Wu, S},
title = {Multi-omics atlas of the bovine coronavirus-infected calf jejunum: reduction of Phocaeicola coprophilus and deoxycholic acid linked to Th17/Treg imbalance.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00997-7},
pmid = {42098175},
issn = {2055-5008},
support = {32272966//National Natural Science Foundation of China/ ; 32573272//National Natural Science Foundation of China/ ; 2452023072//Chinese Universities Scientific Fund/ ; 2024-KFKT-031//National Center of Technology Innovation for Dairy/ ; 2025JH-ZRKX-0639//General Project of the Natural Science Foundation of Xi'an, Shaanxi Province/ ; },
abstract = {Optimal calf rearing is fundamental for ensuring efficient milk production. Bovine coronavirus (BCoV) poses a significant threat to calf health and leads to substantial economic losses in the dairy industry. However, the mechanisms by which the intestinal mucosal microbiome regulates the host immune response during infection remain unclear. In this study, we constructed a high-resolution map of the jejunal mucosal microenvironment in BCoV-infected calves. Our findings revealed that BCoV infection led to severe microbial dysbiosis, characterized by a marked reduction in Phocaeicola coprophilus (formerly known as Bacteroides coprophilus) and decreased secondary bile acid, especially deoxycholic acid (DCA). Concurrently, enrichment of harmful microbiota correlated with increased arachidonic acid metabolites. At the host level, BCoV infection altered the composition of jejunal mucosal cells and affected metabolic and immune-related pathways. The differentiation of CD4[+] T cells played a central role in the jejunum's response to BCoV infection. By integrating these metabolic alterations with dynamic host cellular responses, we suggested a putative that DCA deficiency might contribute to the pathological polarization of CD4[+] T cells toward a Th17 phenotype while suppressing Treg differentiation. These findings suggest that restoring the Phocaeicola coprophilus-affected bile acid transformation might represent a promising therapeutic strategy for BCoV infection.},
}

@article {pmid42098416,
year = {2026},
author = {Albaugh, VL and Devarakonda, SLS},
title = {Surgically reshaping the gut microbiome.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42098416},
issn = {2522-5812},
}

@article {pmid42098417,
year = {2026},
author = {Olsson, LM and Borgeraas, H and Chakaroun, RM and Hofsø, D and Hertel, JK and Dwibedi, C and Mitteregger, M and Holst, JJ and Tremaroli, V and Hjelmesæth, J and Bäckhed, F},
title = {Gut microbiota responses to bariatric surgery are associated with metabolic outcomes and type 2 diabetes remission.},
journal = {Nature metabolism},
volume = {},
number = {},
pages = {},
pmid = {42098417},
issn = {2522-5812},
support = {2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; 2022-06725//Vetenskapsrådet (Swedish Research Council)/ ; 2013-07800//Vetenskapsrådet (Swedish Research Council)/ ; 615362//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; NNF13OC0008163//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; METABASE//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 2017.0026//Knut och Alice Wallenbergs Stiftelse (Knut and Alice Wallenberg Foundation)/ ; 17CVD01//Fondation Leducq/ ; },
abstract = {Bariatric surgeries, such as Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG), improve obesity and type 2 diabetes (T2D). Both surgeries affect the gut microbiota, but their contribution to T2D remission remains unclear. In this subanalysis (RYGB, n = 39; SG, n = 38) of the randomized controlled Oseberg trial (NCT01778738), in which participants underwent either RYGB or SG surgery, we profiled the faecal microbiome of individuals with obesity and T2D before and 12 months after surgery. We show that both surgeries altered the microbiome in the same direction, but with larger changes after RYGB. The SG-associated altered microbiome composition correlated positively with circulating glucagon-like peptide 1 levels, beta-cell function and 5 year T2D remission. Remission was also linked to increased gene richness and metabolic potential for fermentation, methanogenesis and butyrate production. Notably, these associations persisted after accounting for the extent of weight loss. Our findings indicate that surgery-specific microbial adaptations influence metabolic improvements and may help to explain heterogeneity in T2D remission after bariatric surgery.},
}

@article {pmid42098439,
year = {2026},
author = {Prendergast, PJ and Bishop, HV and Herbold, CW and Verdu, EF and Dobson, RCJ and Day, AS and Ogilvie, OJ},
title = {Comprehensive cross-cohort analysis reveals global gut microbiome signatures of celiac disease.},
journal = {Communications medicine},
volume = {},
number = {},
pages = {},
doi = {10.1038/s43856-026-01627-1},
pmid = {42098439},
issn = {2730-664X},
abstract = {BACKGROUND: Celiac disease affects ~1-2% of people and remains incurable, requiring lifelong dietary restriction. The gut microbiome is thought to contribute to the development and progression of celiac disease. However, findings across previous studies are fragmented, making it difficult to understand exactly how the gut microbiome is involved.

METHODS: We integrate over 900 samples from global datasets spanning different disease stages (before onset, during active disease, and after treatment), body sites, and research methods. Datasets produced using both 16S rRNA gene sequencing and shotgun metagenomics profile the gut microbiome. Alpha and beta diversity analyses and differential abundance testing identify consistent changes in bacterial communities linked to celiac disease. Machine learning tests how well microbiome data predicts disease status.

RESULTS: Here, we show that celiac disease is not marked by large changes in gut microbiome diversity. Instead, there are subtle, consistent changes in specific bacteria, including a reduction in beneficial butyrate producers (Faecalibacterium, Prevotella, Agathobacter, Gemmiger), changes in mucin-associated microbes (Akkermansia muciniphila), and an increase in potentially harmful bacteria (Helicobacter, Campylobacter, Haemophilus parainfluenzae). These changes are seen before and during active disease and persist on a gluten-free diet. Microbiome-based disease prediction is moderately accurate for active disease and weaker for prospective performance, likely constrained by training data.

CONCLUSIONS: Our findings suggest that celiac disease is linked to specific changes in gut bacteria that are not fully resolved by diet alone. Future treatments may need to focus on restoring healthy gut bacteria, not just avoiding gluten, to better manage the disease.},
}

@article {pmid42083348,
year = {2026},
author = {Valentini, M and Valentini, GM and Akkawi, I and Zeppa, SD and Bartolacci, A and Pegreffi, F and Zmerly, H},
title = {The Interplay between Osteoarthritis and the Microbiome-joint Axis: A Systemic Perspective on Novel Therapeutic Targets.},
journal = {Current rheumatology reviews},
volume = {},
number = {},
pages = {},
doi = {10.2174/0115733971450825260423042902},
pmid = {42083348},
issn = {1875-6360},
abstract = {Osteoarthritis (OA) is a chronic and progressive joint disease involving the articular cartilage, synovium, subchondral bone, and ligaments, ultimately leading to pain, dysfunction, and, in advanced stages, joint destruction. Several factors contribute to the development and progression of OA, including genetic predisposition, biomechanical stress, metabolic imbalance, and chronic low-grade inflammation. Recently, a novel factor has emerged: the gut microbiome. Gut dysbiosis, defined as an alteration in gut microbiota homeostasis, can disrupt immune, metabolic, and inflammatory pathways, promoting systemic inflammation and accelerating degenerative changes in joint tissues. Conversely, restoration of a balanced gut microbiota may play a protective role and represent a promising avenue for innovative therapeutic strategies. The aim of this review is to analyse the relationship between gut dysbiosis and osteoarthritis, and to discuss potential therapeutic approaches targeting the microbiome to prevent disease progression.},
}

@article {pmid42083431,
year = {2026},
author = {Ebersole, JL and Kirakodu, SS and Gonzalez, OA},
title = {Transcriptomic analysis of gingival tissues in resolved experimental periodontal lesions of nonhuman primates.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70048},
pmid = {42083431},
issn = {1943-3670},
support = {P20GM103538/NH/NIH HHS/United States ; P40RR03640//Caribbean Primate Research Center/ ; //Microarray Core of the University of Kentucky/ ; },
abstract = {BACKGROUND: This study used a preclinical model of experimental periodontitis in nonhuman primates to evaluate the biological features of resolved periodontal lesions.

METHODS: Macaca mulatta (rhesus monkeys) were age-stratified into young [≤3 years (7-10-year-old humans)], adolescent/young adult [3-7 years (12-25-year-old)], adults [12-15 years (40-50-year-old)], and aged [17-23 years (60-80-year-old)]. The samples were also analyzed based on sex or matrilineal derivation. The gingival transcriptome was evaluated using microarray analyses on tissue biopsies from healthy tissues and at resolution (i.e., clinical improvement).

RESULTS: Resolution sites showed clinical improvement, as well as patterns of increased or decreased gene expression in resolution versus healthy tissues in all age groups. These differences represented a large array of adaptive immune genes that were elevated in resolution, with decreased metabolic, regulatory, structural, and transcription factor gene expression in the resolution samples. Many of these genes were common to all age groups or sex/matriline, thus suggesting some fundamental core profile of affected genes that discriminate healthy from lesion resolution tissues.

CONCLUSIONS: Irrespective of age, the biology of periodontal lesion resolution tissues is distinct from healthy tissues. Despite a robust inflammatory response to the ligature-induced microbiome changes during experimental periodontitis, younger individuals showed significantly less destructive disease and different transcriptome profiles that could reflect improved lesion resolution. While sex and matriline affected the gene expression patterns, these generally overlapped with the prominent genes identified for resolution versus health across age groups. Highly affected genes could be considered biomarkers for resolved tissues, linking clinical and biological resolution of periodontal lesions.},
}

@article {pmid42083540,
year = {2026},
author = {YuXuan, G and Iqbal, MK and Khan, B and Khan, H and Ud Din Shah, SS and Al-Hussain, F and Kiyani, MM and Bashir, S},
title = {The Gut-Brain Connection: Exploring the Connection Between the Gastrointestinal System and Parkinson's Disease.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273419693251206130059},
pmid = {42083540},
issn = {1996-3181},
abstract = {Parkinson's disease (PD) is a complex neurodegenerative disorder characterized by motor and non-motor symptoms. Recent studies indicate that the gut-brain axis contributes to both the initiation and progression of PD, a disorder that primarily affects the central nervous system. This article reviews current research on the interaction between the central nervous system and the gastrointestinal tract in PD. The vagus nerve, areas of the enteric nervous system (ENS), systemic inflammation, and the microbiome are all involved in this interaction. For example, recent studies have shown PD-related effects such as abnormal distribution of gut bacteria, increased gut barrier permeability, and α-synuclein transport from the gut to the brain. A comprehensive evaluation of motor and non-motor symptoms was conducted. Additionally, we explored drugs that specifically target the gastrointestinal system, the possible gastrointestinal symptoms of PD, and how these symptoms may serve as early indicators of the disease. Our article also discusses dietary modifications, probiotics, and fecal microbiota transplantation as potential treatments for PD. By reviewing clinical and basic scientific research as well as translational applications, this article highlights the relationship between the central nervous system and the digestive system in PD. A better understanding of this complex connection may lead to improved detection and treatment of this debilitating disease and offer new opportunities for prevention and therapy. Finally, this paper suggests directions for further research in this area.},
}

@article {pmid42083599,
year = {2026},
author = {Kozlova, AS and Zgoda, AV and Petushkova, NA and Bolochenkov, NA and Zgoda, VG and Salnitska, MA and Kazakov, DV and Lisitsa, AV},
title = {The Microbiomic Metaproteome of the Taiga Tick Ixodes persulcatus from the Tyumen Region.},
journal = {Acta naturae},
volume = {18},
number = {1},
pages = {55-63},
pmid = {42083599},
issn = {2075-8251},
abstract = {Metagenomic studies have revealed the taxonomic composition of the taiga tick (Ixodes persulca tus) microbiome, whereas metaproteomic data has provided information on the biochemically active fraction of the microbial community residing in the tick. The aim of this study was to characterize the biological pro cesses taking place within the microbiome of the taiga tick I. persulcatus using a metaproteomic approach. To expand the range of identifiable proteins, we used two trypsin concentrations in sample preparation for mass spectrometric analysis. The metaproteomes of unfed female and male ticks were analyzed, which ena bled identification of protein products encoded by 2,100 genes from microorganisms belonging to 203 bacteri al and fungal species. Increased abundance of proteins associated with Ascomycota fungi, particularly abun dant in females, were detected. Proteins from the pathogenic Rickettsia and Borrelia species were identified. These findings enable a transition from a taxonomic metagenomic description to a functional analysis of the microbial consortium role in the physiology of the vector tick, particularly given the identified microbiota differences related to the tick sex.},
}

@article {pmid42083728,
year = {2026},
author = {Gaskin, PS and Chami, PS},
title = {Low Weight Loss Response to Incretin Analogs: A Systematic Review.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70145},
doi = {10.1111/obr.70145},
pmid = {42083728},
issn = {1467-789X},
abstract = {The development of GLP-1 and GIP analogs has been a significant breakthrough in type 2 diabetes and obesity pharmacotherapy. However, individual responses to these medications can vary widely. This systematic review examines factors associated with low or no weight loss response to GLP-1 and GIP analogs. Key predictors of poor response include higher baseline body weight, BMI, HbA1c, and insulin resistance. Genetic factors, such as variants in the GLP1R gene, may also influence treatment outcomes. Metabolic health status, particularly glycemic control and insulin sensitivity, plays a crucial role in determining weight loss efficacy. Adherence to medication regimens is strongly associated with treatment success, with each additional month of treatment linked to greater weight loss. Lifestyle factors, including dietary habits and physical activity, can modulate responses to these medications. Emerging evidence suggests that gut microbiome composition may mediate weight loss outcomes. Demographic factors such as male sex and older age are associated with lower weight loss responses. Understanding these predictors is essential for optimizing treatment strategies, setting realistic expectations, and moving towards a precision medicine approach in obesity care. Further research is needed to validate these findings in diverse populations and develop practical tools for clinical decision-making.},
}

@article {pmid42083785,
year = {2026},
author = {Wu, Y and Liu, J and Ren, Y and Zou, C},
title = {Unravelling the Gut-Skin Axis in Chronic Urticaria: Dysbiosis, Metabolites and Immunological Mechanisms.},
journal = {Experimental dermatology},
volume = {35},
number = {5},
pages = {e70261},
doi = {10.1111/exd.70261},
pmid = {42083785},
issn = {1600-0625},
support = {2025C02080//the Key Research and Development Plan of Zhejiang Province/ ; WKJ-ZJ-2409//the National Health Commission Scientific Research Fund/ ; },
mesh = {Humans ; *Dysbiosis/immunology ; *Gastrointestinal Microbiome ; Animals ; *Chronic Urticaria/immunology/microbiology/metabolism ; *Skin/immunology/metabolism ; Mice ; Fatty Acids, Volatile/metabolism ; Mast Cells/immunology ; },
abstract = {Although the core pathophysiological pathways of chronic urticaria (CU) are increasingly understood, the upstream triggers and factors contributing to disease chronicity remain poorly understood. Emerging evidence suggests that gut microbiota dysbiosis represents a potentially modifiable upstream factor, which has been predominantly investigated in patients with chronic spontaneous urticaria (CSU). Multi-omics and Mendelian randomization studies have provided convergent evidence linking gut dysbiosis to systemic inflammation and mast cell instability. This is characterized primarily by the depletion of short-chain fatty acid (SCFA)-producing taxa (e.g., Faecalibacterium, Roseburia and Bifidobacterium) and the relative enrichment of pro-inflammatory Proteobacteria (particularly Enterobacteriaceae). Mechanistically, these alterations may lower the mast cell activation threshold and promote systemic immune dysregulation through specific metabolic shifts, such as the depletion of SCFAs and unsaturated fatty acids, and the translocation of endotoxins (e.g., lipopolysaccharide) due to compromised intestinal barrier function. In this review, we discuss how the use of Mendelian randomization (MR) and germ-free mouse models can advance the gut-urticaria axis (with a primary focus on CSU) from mere correlation to causation, while highlighting the crucial need to account for clinical confounders. Finally, we evaluate the clinical translational potential and associated challenges of microbiome-targeted interventions (e.g., probiotics, faecal microbiota transplantation) as novel adjuvant therapies.},
}

Humans
*Dysbiosis/immunology
*Gastrointestinal Microbiome
Animals
*Chronic Urticaria/immunology/microbiology/metabolism
*Skin/immunology/metabolism
Mice
Fatty Acids, Volatile/metabolism
Mast Cells/immunology

@article {pmid42083883,
year = {2026},
author = {Rutigliani, G and Cross, TL and de Jong, E and Glover, ES and Mendoza, ID and Adisa, M and Tomoo, K and Zhou, X and Mattes, RD},
title = {GLP-1 Receptor Agonists and Weight Loss: A Critical Review of Mechanisms.},
journal = {Obesity reviews : an official journal of the International Association for the Study of Obesity},
volume = {},
number = {},
pages = {e70148},
doi = {10.1111/obr.70148},
pmid = {42083883},
issn = {1467-789X},
abstract = {GLP-1 receptor agonist medications have the potential to promote marked weight loss, but maximal and sustained benefit may be compromised by poor compliance and cessation of use. Development of next-generation medications that address current obstacles to effective use and development of effective adjunct treatments will benefit from better characterization of their mechanisms of action. This narrative review critically assesses eight purported mechanisms including modulation of appetite, chemosensory function, cravings/aversions, food noise, gastric emptying, the microbiome, incretin activity, and energy expenditure. Current evidence does not support a single dominant mechanism; a combination of subtle effects may underlie the efficacy of these medications. However, as experience with these medications and methods to assess their effects grows, it should be possible to better determine the relative importance of these and possibly other mechanisms.},
}

@article {pmid42083901,
year = {2026},
author = {Gago-Ferrero, P and Boehm, AB and Hsu-Kim, H and Li, XD and Gibson, JM and Vrijheid, M and Wang, B and Zimmerman, J},
title = {The Human Exposome: Integrating the Environment, Human Health, and Society for the Next 60 years.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c03080},
pmid = {42083901},
issn = {1520-5851},
abstract = {The exposome framework promises comprehensive characterization of chemical, physical, and biological exposures shaping human health, yet the measurement capacity now vastly outpaces interpretation and action. Here, we synthesize emerging frontiers that define the translation of exposome science into prevention: moving from "chemical dark matter" in high-resolution mass spectrometry toward functional exposomics; integrating the microbial exposome as both the target and modulator of exposures; deploying AI-enabled causal inference to bridge molecular precision with population-scale patterns; and embedding exposome evidence into proactive interventions, green chemistry, environmental redesign, and environmental justice frameworks. Progress over the next six decades will depend not only on measurement comprehensiveness but also on our capacity to shift from documenting environmental harm to designing healthier environments.},
}

@article {pmid42084201,
year = {2026},
author = {Ebihara, S and Kamada, N},
title = {The Oral-Gut Axis: Bidirectional Interactions Between Microbiome and Diseases.},
journal = {Journal of periodontal research},
volume = {},
number = {},
pages = {},
doi = {10.1111/jre.70116},
pmid = {42084201},
issn = {1600-0765},
support = {DK108901/NH/NIH HHS/United States ; DK119219/NH/NIH HHS/United States ; CA288546/NH/NIH HHS/United States ; JP21gm6310023//Japan Agency for Medical Research and Development/ ; JP25gm4010030//Japan Agency for Medical Research and Development/ ; JP23H00404//Japan Society for the Promotion of Science/ ; },
abstract = {Increased colonization of typically oral microorganisms is frequently observed in the gut mucosa or lumen of individuals with gastrointestinal disorders, including patients with inflammatory bowel disease and colorectal cancer. Accumulating clinical and experimental evidence indicates that this phenomenon, known as "gut oralization," plays an important role in the pathogenesis of these diseases. Although several physiological barriers normally restrict the translocation and ectopic colonization of microorganisms from the oral cavity to the gut, certain oral pathobionts-often enriched in individuals with oral diseases such as periodontitis-have evolved specialized strategies to overcome these defenses. This review examines the bidirectional interactions through which bacterial traits, including unique adhesion systems and metabolic adaptations, support colonization and expansion within the gastrointestinal tract, as well as how disease-associated alterations in the gut environment and increased host vulnerability facilitate ectopic colonization by bacteria of oral origin. By integrating clinical and mechanistic evidence, this review highlights the potential of targeting the oral-gut microbial axis as a therapeutic approach for preventing and treating chronic gastrointestinal disorders.},
}

@article {pmid42084382,
year = {2026},
author = {Van Beeck, W and Lemos, MLP and Niesen, AM and Finnegan, P and Shih, TM and Ho, A and Rossow, HA and Marco, ML},
title = {Variations in cow milk and teat skin microbiota across the lactation cycle with intramammary cephalosporin use at dry-off.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0231225},
doi = {10.1128/aem.02312-25},
pmid = {42084382},
issn = {1098-5336},
abstract = {Cephalosporins and other broad-spectrum antibiotics are frequently administered prophylactically into the udder when dairy cows end their lactation cycle, termed dry-off, to reduce mastitis risk. However, the use of antibiotics on cows that do not have signs of infection may result in the selection of antibiotic-resistant microorganisms and negatively alter the udder microbiome. In this study, the effects of intramammary cephalosporin therapy with Cephapirin (CB) or Ceftiofur (CH) on milk and teat skin microbiota were examined for three dairies in California. Intramammary injections were given to healthy cows with high somatic cell counts (>200,000 cells/mL), indicative of infection. Samples were collected at dry-off (before treatment), 7 days later, and 55-75 days in milk (DIM) in the next lactation cycle. Dairy (milk: R[2] = 6.22, skin: R[2] = 7.56) and day of sampling (milk: R[2] = 4.74 and skin: R[2] = 3.77) had the highest impact on the milk and skin microbiota. CB or CH use was associated with a small but significant impact on milk microbiota beta-diversity (Bray-Curtis, P =0.003, R[2] = 1.4%), but no effect was observed on the skin. At one dairy (Dairy 3), milk from cows receiving CB and CH had reduced proportions of Staphylococcaceae at 55-75 DIM compared to untreated cows. Overall, antibiotic use did not result in large significant (beneficial or harmful) changes in bacterial diversity in milk or on the teat skin; instead, the microbiota differences were mainly influenced by the time and location of sampling.IMPORTANCEThe use of antibiotics in agriculture is under increasing scrutiny due to the rising spread of antimicrobial-resistant bacteria. Our study showed that common preventative antibiotic intramammary treatment of cows with cephalosporins at the end of their lactation (dry-off) had minimal effects on the milk and teat skin microbiota of asymptomatic cows with high somatic cell counts.},
}

@article {pmid42084394,
year = {2026},
author = {Liu, C and Ribeiro, MM and Yang, J and Li, L and Li, J and Chen, X and Wang, Y and Wang, L-L and Wang, B and Zhou, Y and Zhang, J and Jiang, J and Lin, J and Delbaje, E and Xu, J-F and Goldman, GH and Liang, S},
title = {Multi-omics profiling of fungal balls in chronic pulmonary aspergillosis patients reveals microbiome dynamics and metabolic adaptations.},
journal = {mBio},
volume = {},
number = {},
pages = {e0034826},
doi = {10.1128/mbio.00348-26},
pmid = {42084394},
issn = {2150-7511},
abstract = {Fungal balls (aspergillomas) are a debilitating complication of chronic pulmonary aspergillosis, but their functional biology as multi-kingdom ecosystems is poorly understood. Through integrated multi-omics analysis of 61 patient-derived fungal balls, we reveal their complex ecology. While Aspergillus fumigatus dominates the fungal niche (59% of patients), bacterial co-colonization is ubiquitous, primarily by Pseudomonas aeruginosa and Haemophilus influenzae. Metabolomics and metatranscriptomics unveil a structured division of labor and active warfare, including metabolic cross-feeding, competition for iron, and reciprocal antagonism via secondary metabolites, such as fumagillin and fumigaclavine C produced by A. fumigatus. Host metabolomics and transcriptomics revealed a potent but dysregulated human immune response, characterized by neutrophil activation and failed resolution. Our findings redefine aspergilloma not as a mere fungal aggregate, but as a resilient polymicrobial biofilm across kingdoms, in which synergistic and antagonistic inter-kingdom interactions drive pathogenesis and chronicity, suggesting new therapeutic strategies targeting the pathogenic consortium.IMPORTANCEChronic pulmonary aspergillosis (CPA) and its hallmark fungal balls (aspergillomas) represent a debilitating and difficult-to-treat respiratory disease, affecting millions worldwide. Here, we provide the first integrated multi-omics profile of surgically resected fungal balls from 61 CPA patients, revealing these structures not as mere fungal colonies, but as resilient, cross-kingdom biofilms teeming with bacterial co-colonizers, particularly Pseudomonas aeruginosa and Haemophilus influenzae. Our findings uncover a dynamic battlefield where fungi and bacteria engage in metabolic cross-feeding, chemical warfare, and competition for nutrients such as iron. We demonstrate that the host mounts a potent but dysregulated immune response characterized by chronic neutrophilic inflammation and failed resolution, driving tissue damage and disease persistence. Our data provide a foundation for novel therapeutic strategies aimed at disrupting microbial synergy, modulating host inflammation, and breaking the cycle of chronic infection, an approach that could significantly improve outcomes for patients with this refractory disease.},
}

@article {pmid42084439,
year = {2026},
author = {Wu, H and Han, Y and Wen, Z and Liu, WV and Tu, N and Yang, W and Li, J and Zha, Y},
title = {Higher Abundance of Genus Desulfovibrio May Underlie Resistance to Antipsychotic-Induced Weight Gain in Schizophrenia.},
journal = {Schizophrenia bulletin},
volume = {52},
number = {3},
pages = {},
pmid = {42084439},
issn = {1745-1701},
support = {JCZRQNB202600163//Natural Science Foundation of Hubei Province/ ; 2022YFC2009900//National Key R&D Program of China/ ; 2022YFC2009905//National Key R&D Program of China/ ; },
mesh = {Humans ; *Schizophrenia/drug therapy/microbiology ; *Gastrointestinal Microbiome/drug effects ; *Antipsychotic Agents/adverse effects/pharmacology ; Male ; Female ; Adult ; *Weight Gain/drug effects ; *Obesity/microbiology/chemically induced ; *Desulfovibrio ; Middle Aged ; Young Adult ; Feces/microbiology ; },
abstract = {BACKGROUND: Obesity is prevalent among schizophrenia (SZ) patients receiving long-term antipsychotic treatment, yet a subset of patients remains lean or maintains a normal weight. While prior studies have linked the gut microbiome to antipsychotic-induced weight gain, its role in maintaining weight stability among non-obese SZ patients remains largely unexplored.

STUDY DESIGN: We recruited 177 participants for the discovery cohort, including chronically antipsychotic-treated SZ patients with or without obesity, as well as healthy controls (HCs) matched by weight status. Additionally, we enrolled 20 first-episode, drug-naïve SZ (FSZ) patients with normal weight to assess their weight changes during one year of antipsychotic treatment. Fecal 16S rRNA sequencing, combined with untargeted metabolomics, was conducted to characterize gut microbiota and metabolite profiles in non-obese SZ patients, and to investigate their association with antipsychotic-induced weight changes.

STUDY RESULTS: In total, 15 bacterial genera were identified. Among them, the genera Bacteroides, Dialister, and Pseudomonas exhibited the lowest abundance in non-obese SZ patients, whereas the genus Oscillospira showed the highest abundance. Notably, Desulfovibrio was more abundant in non-obese SZ patients and HCs than in their obese counterparts. This microbial profile was accompanied by enhanced tryptophan metabolism. In FSZ patients, higher baseline levels of Desulfovibrio were linked to less weight gain after 1 year of antipsychotic treatment. Moreover, Desulfovibrio abundance correlated positively with fecal indoleacetic acid levels and inversely with serum tryptophan concentrations.

CONCLUSIONS: These findings suggest a potential protective role of genus Desulfovibrio against antipsychotic-induced weight gain, possibly through modulation of tryptophan metabolism.},
}

Humans
*Schizophrenia/drug therapy/microbiology
*Gastrointestinal Microbiome/drug effects
*Antipsychotic Agents/adverse effects/pharmacology
Male
Female
Adult
*Weight Gain/drug effects
*Obesity/microbiology/chemically induced
*Desulfovibrio
Middle Aged
Young Adult
Feces/microbiology

@article {pmid42084538,
year = {2026},
author = {Jongen, R and Gribben, PE and Erickson, KR and Marzinelli, EM},
title = {Ocean warming indirectly affects seagrass performance through effects on sediment microbial communities.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71195},
pmid = {42084538},
issn = {1469-8137},
support = {DP240100566//Australian Research Council/ ; LP200200220//Australian Research Council/ ; },
abstract = {Belowground microbes are increasingly recognised as mediators of plant responses to stress, but it remains unclear whether the thermal histories of marine plants and their associated belowground microbes influence plant performance under ocean warming. We conducted a common-garden field experiment at a long-term warmed site in Lake Macquarie (NSW, Australia, > 30 yr, 1-3°C warming), to test the effects of sediment origin (ambient vs warm-origin), plant origin (ambient vs warm-origin) and microbial disruption (intact vs disrupted rhizosphere and bulk sediment microbial communities) on seagrass (Zostera muelleri) performance. Both plant origins had lower aboveground biomass in intact warm-origin sediments, but warm-origin plants recovered when bulk sediment microbial communities were disrupted, indicating that warming-altered sediment microbial communities can suppress seagrass performance. Disrupted warm-origin sediments were enriched in sulphide-oxidising bacteria, which likely contributed to enhanced performance. In warm-origin sediments, rhizosphere bacterial communities were similar across plant origins, indicating that sediments shape rhizosphere bacterial assembly. Rhizosphere microbial disruption had no effect on plant performance. We show that ocean warming can shape sediment microbial communities in ways that suppress seagrass performance, suggesting that sediment microbial communities can override plant thermal history and act as hidden constraints on seagrass tolerance to warming.},
}

@article {pmid42084709,
year = {2026},
author = {Komal, A and Ilyas, D and Khan, MU and Rehman, MKU and Hassan, T and Ayub, H and Naqi, N and Ullah, N and Ilyas, U},
title = {Multi-modal therapeutic approaches to inflammatory bowel disease: plant-derived compounds, nanoparticle drug delivery systems, and gene-based interventions.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42084709},
issn = {1573-4978},
mesh = {Humans ; *Inflammatory Bowel Diseases/therapy/genetics/drug therapy ; *Nanoparticle Drug Delivery System/therapeutic use ; *Genetic Therapy/methods ; *Drug Delivery Systems/methods ; Nanoparticles ; Animals ; RNA, Small Interfering ; MicroRNAs/genetics ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder primarily affecting the gastrointestinal tract. The pathogenesis arises from complex interactions among genetic predisposition, immune dysregulation, and gut microbiota alterations. Recent advances in molecular biology, genomics, and microbiome research have identified novel therapeutic targets, enabling the development of innovative treatment strategies. Natural products derived from plants offer bioactive compounds with anti-inflammatory, antioxidant, and immunomodulatory properties, gaining attention for IBD symptom management. Conventional therapeutic management includes aminosalicylates, immunomodulators, corticosteroids, and biologics; however, 30-50% of patients show inadequate response, and oral drug delivery faces challenges due to gastrointestinal environmental heterogeneity. Recent years have witnessed substantial advances in nanoparticle-based drug delivery systems for IBD, offering improved targeting capabilities, enhanced therapeutic efficacy, and better tolerability through stimuli-responsive platforms (ROS-sensitive, pH-responsive) and active targeting strategies. Nanoparticle-mediated gene therapy, including siRNA, miRNA, and emerging CRISPR-based approaches, represents a paradigm-shifting strategy for modulating aberrant gene expression in IBD. This comprehensive review synthesizes the current understanding of IBD pathophysiology, evaluates both conventional and emerging therapeutic approaches, and provides critical analysis of advanced nanoparticle delivery systems and gene-based therapeutic strategies.},
}

Humans
*Inflammatory Bowel Diseases/therapy/genetics/drug therapy
*Nanoparticle Drug Delivery System/therapeutic use
*Genetic Therapy/methods
*Drug Delivery Systems/methods
Nanoparticles
Animals
RNA, Small Interfering
MicroRNAs/genetics

@article {pmid42084747,
year = {2026},
author = {Kumar, V and Nautiyal, CS},
title = {Harnessing the plant microbiome: innovation towards sustainable agriculture and ecological resilience.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42084747},
issn = {1572-9699},
mesh = {*Microbiota ; Soil Microbiology ; Climate Change ; *Crops, Agricultural/microbiology/growth & development ; *Agriculture/methods ; *Plants/microbiology ; Biodiversity ; Ecosystem ; Plant Breeding ; },
abstract = {Assimilation of plant-microbiome synergism into contemporary sustainable approaches offers transformational prospective for augmenting crop production, and environment resilience. Efficient microbiome enhances nutrients acquisition, encouraging plant's growth, and mitigate diverse stressors. Synthetic microbial communities could be another strategy to augment crop yield by improving bioinoculants activity, regulating and reinstating microbial diversity. Long-term agricultural output depends on microbiome's intervened activities, such as nutrients acquisition, thereby lowering chemical fertilizers necessity. Microbes also contribute to climate change mitigation by endorsing soil carbon stowage and minimizing release of greenhouse gases via enhanced nutrients use efficacy. Developments in sustainable crop breeding and genomics have facilitated the recognition of plant traits and genetic loci that influence alliances of valuable microbes. Integration of plant-microbiome breeding tactics might lead to optimization of microbiome selection in plant varieties, thus improving yield and stress resilience. Such approaches will conserve biodiversity, restore ecosystem by nurturing functional microbiome population, supporting plant's diversity and soil health. Microbiome are also able to improve degraded soils recovery, plant's establishment, parallelly safeguarding ecosystem restoration. The integration of microbial technology in crops could enhance the nutritional value and safety of food while supporting environmental sustainability and human health. Understanding microbiome-plant-climate change interactions is critical for developing adaptive strategies that enhance resilience to environment and climate variability, ensure sustainable food systems, and promote ecological balance in a changing global environment.},
}

*Microbiota
Soil Microbiology
Climate Change
*Crops, Agricultural/microbiology/growth & development
*Agriculture/methods
*Plants/microbiology
Biodiversity
Ecosystem
Plant Breeding

@article {pmid42084764,
year = {2026},
author = {Joshi, G and Khannam, KS},
title = {Marine microbiomes and their expanding role in biotechnological potential: a systematic review.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42084764},
issn = {1432-072X},
mesh = {*Microbiota ; *Biotechnology ; *Seawater/microbiology ; *Bacteria/metabolism/classification/genetics/isolation & purification ; Ecosystem ; Biodegradation, Environmental ; },
abstract = {Marine bacteria are present almost everywhere in the ocean environment and are essential to many biogeochemical processes. The perspectives of ecologists and evolutionary biologists on the significance of microbes in ecosystem function are shifting as a result of exploring the marine microbiomes. This is especially true in ocean habitats, where microbes comprise the bulk of the biomass and are responsible for the majority of the planet's key biogeochemical cycles, including those that influence the global climate. Emerging research suggests that many ecosystem services provided by coastal marine environments depend on intricate interactions between groups of microbes and the environment or their hosts. The structure, variety, and functional capability of marine microbial populations have been revealed on a global scale thanks to recent developments in molecular ecology techniques. Over-recent-decades, industrialization and urbanization have led to widespread contamination of oceans. These contaminants accumulate in seawater and sediments, particularly in coastal areas, posing risks to marine ecosystems and human health. Marine microorganisms possess diverse catalytic abilities and extreme environmental tolerance, making them suitable for bioremediation of toxins. Effective-degradation of pollutants often depends on syntrophic-interactions within microbial communities, highlighting the importance of understanding their collaboration and communication for marine resource management. Here, we assess the current level of knowledge about marine microbiome research and highlight key issues within this developing field of study. The review aims to enhance understanding of marine microbiome's roles and potential uses in biogeochemical analysis, biotechnology, and environmental remediation, which could support sustainable and circular business models for future generations.},
}

*Microbiota
*Biotechnology
*Seawater/microbiology
*Bacteria/metabolism/classification/genetics/isolation & purification
Ecosystem
Biodegradation, Environmental

@article {pmid42084801,
year = {2026},
author = {Liu, G and Chen, K and Li, J and Zhang, K and Niu, G and Ding, Y and Lv, Y and Tian, Q and Cao, Z and Wang, H and Jia, J and Zhang, G and An, Y},
title = {Deciphering potential significances of biliary microbiome in cholelithiasis and cholangiocarcinoma.},
journal = {Antonie van Leeuwenhoek},
volume = {119},
number = {6},
pages = {},
pmid = {42084801},
issn = {1572-9699},
support = {No. 25A330005//the Key Scientific Research Projects of Henan Higher Education Institutions/ ; No. 202510475073, 202510475143, 202510475139, XJ2025344, XJ2025363//the Innovation Project for College Students of Henan University/ ; No. 262102311042//the Program for Science and Technology Development in Henan Province/ ; },
mesh = {*Cholangiocarcinoma/microbiology ; *Cholelithiasis/microbiology ; Humans ; *Microbiota ; *Bile Duct Neoplasms/microbiology ; Bacteria/classification/genetics/isolation & purification ; Computational Biology ; *Biliary Tract/microbiology ; High-Throughput Nucleotide Sequencing ; },
abstract = {BACKGROUND: This study aims to investigate the role of biliary microbiota (defined as the microbial community colonizing the biliary tract, including the gallbladder, intrahepatic and extrahepatic bile ducts) in the pathogenesis of cholelithiasis (CHOL) and cholangiocarcinoma (CCA), with a focus on the associations between microbial communities and these biliary diseases.

METHODS: We conducted a comprehensive bioinformatics analysis using high-throughput sequencing data obtained from the Sequence Read Archive (SRA) database to characterize the composition of microbial communities in patients with CCA and CHOL. We performed operational taxonomic unit (OTU) clustering, statistical analyses and Mendelian randomization (MR) to elucidate the causal relationships between specific bacterial strains and disease outcomes.

RESULTS: Our findings revealed differences in the relative abundance of specific microbial taxa among research groups. The CCA + CHOL group exhibited a significant increase in the abundance of Fusobacteria, particularly Fusobacterium, compared to the Control or CCA group. This suggests a potential pathogenic role for these microorganisms in CHOL formation. Additionally, the CCA group demonstrated a higher diversity index, indicating that increased microbial diversity may contribute to the progression of the disease. MR analysis identified nominally significant statistical associations between specific bacterial strains. However, the presence of pleiotropy in some analyses necessitates caution when interpreting causal relationships.

CONCLUSION: Our study highlights the complex interplay between biliary microbiota and the pathogenesis of CHOL and CCA. Modulating biliary microbiota may represent a promising therapeutic strategy for managing these diseases. Future research should focus on the functional roles of specific taxa in bile metabolism and immune modulation, ultimately improving our understanding of biliary health and disease management.},
}

*Cholangiocarcinoma/microbiology
*Cholelithiasis/microbiology
Humans
*Microbiota
*Bile Duct Neoplasms/microbiology
Bacteria/classification/genetics/isolation & purification
Computational Biology
*Biliary Tract/microbiology
High-Throughput Nucleotide Sequencing

@article {pmid42084812,
year = {2026},
author = {Ma, J and Tong, P and Yang, K and Jia, Y and Liu, Z and Zhao, M and Liu, J and Long, F},
title = {Lactiplantibacillus plantarum Mediated Tryptophan Metabolism to Alleviate Tropomyosin-induced Food Allergy.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42084812},
issn = {1867-1314},
support = {32472454//National Natural Science Fund/ ; YQK[2023]020//Guizhou Provincial Science and Technology Programme for Outstanding Young Talents in Science and Technology/ ; 2024NC-GJHX-04//Key Research and Development Projects of Shaanxi Province/ ; },
abstract = {Food allergy (FA) has become increasingly prevalent, affecting daily life. Probiotics alleviate FA by modulating immune-microbiome interactions. Nevertheless, the key metabolites and mechanisms by which L. plantarum alleviates FA remain unclear. In this study, L. plantarum demonstrated the ability to improve FA by modulating regulatory T/Th1/Th2 balance, modulating gut microbial composition, and regulating gut metabolites. Tropomyosin sensitization was associated with decreased levels of 5-hydroxyindole-3-acetic acid (5-HIAA) in cecum contents, a phenomenon also observed in the serum of FA mice and patients. In vitro experiments showed that tryptophan (Trp), tryptamine, tryptophol, kynurenine, 5-HIAA, and indole-3-acetamide inhibited RBL-2H3 cell degranulation; however, this inhibitory effect was attenuated by the aryl hydrocarbon receptor (AhR) antagonist CH223191. Moreover, in vivo results indicated that dietary supplementation with 5-HIAA or Trp downregulated IgE and cytokine levels in an AhR-dependent manner. This study provided evidence for the positive role of Trp metabolites in alleviating FA.},
}

@article {pmid42085218,
year = {2026},
author = {Wang, LL and Xie, Y and Shen, X and Xu, JF},
title = {Advances in understanding respiratory microbiome are reshaping the management of respiratory diseases.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag017},
pmid = {42085218},
issn = {1535-4970},
}

@article {pmid42085254,
year = {2026},
author = {Zissler, UM and Koczulla, AR},
title = {Lower Airway Dysbiosis Fuels NETosis in NTM Bronchiectasis: Rethinking the Microbiome-Host Axis.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag117},
pmid = {42085254},
issn = {1535-4970},
}

@article {pmid42085326,
year = {2026},
author = {Appuhami, IA and Bajracharya, S and Davis, DA and Bruce, TJ},
title = {Effects of probiotic dose on growth performance, health, and gut microbiota of Pacific white shrimp reared in biofloc conditions.},
journal = {Journal of aquatic animal health},
volume = {},
number = {},
pages = {},
doi = {10.1093/jahafs/vsag001},
pmid = {42085326},
issn = {1548-8667},
support = {58-6010-0-007//United States Department of Agriculture-Agricultural Research Service (USDA-ARS)/ ; ALA016-1-19143//USDA National Institute of Food and Agriculture Hatch/ ; ALA016-1-19102//USDA National Institute of Food and Agriculture Hatch/ ; },
abstract = {OBJECTIVE: This study evaluated the effect of commercial Bacillus spp. probiotics on growth performance, immunity, gut microbiota composition, and disease resistance to Vibrio parahaemolyticus in Pacific white shrimp Litopenaeus vannamei that were reared under biofloc conditions.

METHODS: A 56-d feeding trial was conducted in a static biofloc system with postlarval shrimp (1.00 ± 0.03 g). A total of 1,080 shrimp were randomly assigned to three groups: two treatment levels (recommended dose [PRO × 1] and a doubled dose [PRO × 2]) of a commercial probiotic blend, PRO4000X, alongside a control group (CTL; no probiotics). At the trial end point, hepatopancreas and gut samples were collected for gene expression. Gut samples were also obtained for gut microbiota analysis via 16S ribosomal RNA sequencing, and hemolymph samples were withdrawn to measure the total hemocyte count.

RESULTS: Probiotic applications did not significantly affect growth performance, including final biomass, mean weight, survival, and feed conversion ratio under the experimental conditions. The probiotic-treated shrimp exhibited enhanced survival during a V. parahaemolyticus (strain A3) challenge, with significantly lower mortality rates (P < 0.001; 42.5 ± 4.3% for PRO × 1 and 60 ± 6.5% for PRO × 2) relative to the CTL (100 ± 0.00%). Immune parameters, such as total hemocyte count, did not differ. Interestingly, the expression of the antioxidant gene sod (superoxide dismutase) in the shrimp gut was significantly downregulated in the PRO × 1 group relative to the control (P = 0.030), which suggests reduced oxidative stress under probiotic supplementation. The analysis of the gut microbiota revealed differences in alpha diversity, specifically in evenness and Shannon index, which were significantly higher in the PRO × 1 group. The analysis of the bacterial composition also revealed minor shifts in the dominant genera. Notably, Lysobacter was more abundant in the PRO × 1 group, which potentially reflects positive modulation of gut microbial communities in response to probiotic supplementation.

CONCLUSIONS: Overall, the application of PRO4000X probiotics significantly reduced the V. parahaemolyticus infection in the shrimp that were reared in biofloc water and supported the regulation of immunity and microbial communities in the gut. These findings indicate that probiotics potentially help to improve shrimp health when shrimp are cultured in biofloc systems.},
}

@article {pmid42085335,
year = {2026},
author = {Prentice, AM},
title = {Human Milk Bioactives in Breastfeeding: Understanding the Complex Biology of Mother-Child Interactions.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-3},
doi = {10.1159/000551893},
pmid = {42085335},
issn = {1421-9697},
}

@article {pmid42085336,
year = {2026},
author = {Mwaniki, M and Nabwera, HM},
title = {Transition from Breast Milk: When and How?.},
journal = {Annals of nutrition & metabolism},
volume = {},
number = {},
pages = {1-11},
doi = {10.1159/000551169},
pmid = {42085336},
issn = {1421-9697},
abstract = {BACKGROUND: Breastfeeding is the cornerstone of infant and young child nutrition with implications for long-term health and well-being. However, despite having World Health Organization guidance on the transition from exclusive breastfeeding to complementary feeding, in practice it is often fraught with challenges. This review examines the biological and clinical foundations of breastfeeding, addresses the critical questions of when and how to introduce complementary foods and discusses the gaps that hinder optimal infant feeding practices across different geographies. Finally, it highlights the pivotal role of healthcare professionals in guiding safe and responsive feeding transitions.

SUMMARY: Human breast milk is an essential component of the factors that promote optimal child health, growth and neurodevelopment. Evidence supports exclusive breastfeeding for approximately 6 months. Readiness for complementary feeding should be judged by developmental cues rather than chronological age alone. Complementary feeding introduces new nutritional and immunological demands: texture progression supports oral-motor development, timely exposure to allergens may promote tolerance, and micronutrient status is critical. Global variation in infant feeding practices reflects socioeconomic, cultural, and structural barriers that often limit adherence to guidelines. When exclusive breastfeeding is not feasible despite an optimal healthcare provider and family, partial breastfeeding or formula feeding can support infant growth. However, such decisions ideally require guidance from healthcare providers, which may not be readily accessible to all mothers. Transitioning from exclusive breast milk should be viewed as a gradual layering of foods onto an existing nutritional foundation (often provided by breast milk) rather than abrupt weaning. For maternal and child health practitioners, the priority should be to provide person-centred care that is informed by the individual circumstances of the mother-infant dyad. This includes evidence-informed practical advice that is responsive to their needs, supporting exclusive breastfeeding whenever possible, while ensuring access to safe, nutritionally adequate and sustainable alternatives where needed. Aligning health systems, community support, and policy protections is essential to enable families globally to achieve optimal feeding practices.

KEY MESSAGES: Exclusive breastfeeding for about 6 months provides significant nutritional, immunological, and developmental benefits, but readiness for complementary feeding should be guided by developmental cues, not chronological age alone. Complementary feeding should emphasise iron-rich, diverse foods introduced with appropriate texture progression, alongside continued breastfeeding for sustained child health and growth. Implementation gaps persist globally largely due to unaddressed maternal challenges of navigating breastfeeding and the transition to complementary feeding. An interdisciplinary approach with mothers at the core is important in translating global guidelines into context-specific, practical guidance for families.},
}

@article {pmid42085795,
year = {2026},
author = {Kang, S and Han, X and Gao, J and Zhou, T and Yang, X and Zheng, F},
title = {Distribution patterns and driving mechanisms of antibiotic resistance genes and virulence factor genes under the urbanization gradient.},
journal = {Journal of hazardous materials},
volume = {511},
number = {},
pages = {142270},
doi = {10.1016/j.jhazmat.2026.142270},
pmid = {42085795},
issn = {1873-3336},
abstract = {Antibiotic resistance genes (ARGs), as emerging environmental contaminants, have become a global environmental health concern due to their distribution and dissemination across urbanization gradients. This study systematically investigated the diversity, abundance patterns, and driving mechanisms of 173 ARGs, 30 mobile genetic elements (MGEs), and 120 virulence factor genes (VFGs) along a typical urbanization gradient (urban, suburban, and ecological zones) using soil samples collected from Baoding city center to Baiyangdian Lake periphery. High-throughput sequencing and quantitative PCR analyses revealed that suburban areas exhibited significantly higher total relative abundance of ARGs compared to urban and ecological zones (p < 0.05), particularly for aminoglycoside-, fluoroquinolone-, Macrolide-Lincosamide-Streptogramin B-, and multidrug-resistance genes. Suburban soils also showed elevated levels of VFGs associated with Klebsiella pneumoniae, Salmonella enterica, and Escherichia coli (p < 0.05). Notably, significant associations between ARGs and VFGs were observed, with both demonstrating high loads in suburban areas, suggesting these transitional zones may serve as "incubators" for resistant pathogens. Correlation analyses suggest that both biotic (MGEs, microbial communities) and abiotic factors (urbanization, heavy metals, soil properties) may contribute to ARGs and VFGs dissemination, with MGEs appearing to play a central role. Structural equation modeling indicates that urbanization could influence ARGs and VFGs assembly, potentially by altering soil properties, heavy metals, and microbial communities. MGE-mediated horizontal transfer might facilitate ARGs spread, whereas heavy metals and specific microbial taxa may be associated with VFG distribution patterns. These findings provide critical scientific insights into the transmission dynamics of resistance genes during urbanization and offer strategic guidance for developing targeted environmental management policies to mitigate resistance dissemination.},
}

@article {pmid42085931,
year = {2026},
author = {Wang, Z and Wang, Y and Peters, BA and Post, WS and Brown, TT and Palella, FJ and Rinaldo, CR and Witt, MD and Gange, SJ and Kuniholm, MH and Sha, BE and Chichetto, NE and Clish, CB and Gerszten, RE and Hodis, HN and Sharma, A and Anastos, K and Burk, RD and Kaplan, RC and Qi, Q and Hanna, DB},
title = {Multi-omics analysis of the gut microbiome and carotid artery atherosclerosis in men with and without HIV.},
journal = {EBioMedicine},
volume = {127},
number = {},
pages = {106281},
doi = {10.1016/j.ebiom.2026.106281},
pmid = {42085931},
issn = {2352-3964},
abstract = {BACKGROUND: How gut microbiota alterations may contribute to host inflammation and metabolomic profiles affecting atherosclerosis is not fully elucidated, especially in the context of HIV.

METHODS: We examined associations between gut microbial features (measured by shotgun metagenomics) and subclinical carotid atherosclerosis, as assessed by high-resolution B-mode ultrasound, in 359 men from the MACS/WIHS Combined Cohort Study. We measured 822 plasma metabolites using LC-MS/MS, and up to 2866 circulating proteins by the Olink Explore 3072/384 platform (with a primary focus on 617 proteins related to inflammation and immune function).

FINDINGS: Carotid artery plaque was detected in 115/359 men (32%). Adlercreutzia equolifaciens and Eubacterium sp3131 were associated with lower odds of plaque (OR [95% CI] = 0.57 [0.43, 0.77], 0.84 [0.76, 0.93], respectively), while Coprococcus sp13142 was associated with higher odds of plaque (OR [95% CI] = 1.14 [1.06, 1.23]). Results were consistent in men both with and without HIV. A. equolifaciens was positively correlated with HDL cholesterol and inversely correlated with systolic blood pressure. These plaque-associated microbial species were also associated with a range of circulating metabolites and inflammatory proteins. For example, A. equolifaciens positively correlated with the metabolites palmitoyl-EA and mesobilirubinogen, and inversely correlated with the pro-inflammatory chemokine CXCL9, the immune regulator CD160, and IL-24.

INTERPRETATION: We identified gut microbial features associated with carotid artery atherosclerosis, consistent across HIV status; these associations were partially explained by specific microbiota-related metabolites and inflammatory markers. If validated, these findings suggest gut microbiota-related targets for CVD prevention.

FUNDING: The study was funded by the National Heart, Lung, and Blood Institute (U01HL146204-04S1, K01HL169019).},
}

@article {pmid42086047,
year = {2026},
author = {Cai, C and Wang, A and Shao, Q and Zhang, J and Wang, Y and Hu, H and Yuan, K and Li, L and Wang, X and Fang, Q and Ma, Y},
title = {Cryo-EM structures of prevalent gut phage PD491P1 uncover extensive disulfide stabilization and distinct structural adaptations.},
journal = {Structure (London, England : 1993)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.str.2026.04.005},
pmid = {42086047},
issn = {1878-4186},
abstract = {Bacteriophages play crucial roles in modulating the human gut microbiome, yet structural characterization of prevalent gut phages remains limited. Here, we present high-resolution cryo-EM structures of Parabacteroides phage PD491P1, which is one of the most abundant bacteriophages in the human gut. The structures reveal its mature virion organization, including the capsid, head-to-tail interface, and tail tip regions. Strikingly, PD491P1 exhibits an exceptionally extensive disulfide bond network that covalently stabilizes nearly the entire virion. Unique structural features include an elaborate portal-adaptor-terminator interface and distinctive, upward-pointing and flexible tail fibers with multiple putative host recognition domains. These structural adaptations may enable phage PD491P1 to achieve survival and robust infection in the challenging gut environment. These findings expand our understanding of gut phage structural diversity, reveal mechanistic insights into phage stability and infection, and provide a foundation for future development of phage-based microbiome therapeutics.},
}

@article {pmid42086326,
year = {2026},
author = {Azulay, A and Gotesdyner, L and Aharoni-Frutkoff, Y and Focht, G and Talmor, Y and Borenstein, E and Plotkin, L and Orlanski-Meyer, E and Lev-Tzion, R and Ledder, O and Yogev, D and Assa, A and Broide, E and Yerushalmy-Feler, A and Kierkuś, J and Schwerd, T and Wine, E and Turner, D},
title = {Multi-omics-based machine learning model predicts response and guides treatment in Crohn disease: a case study in nutritional therapy.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag060},
pmid = {42086326},
issn = {1536-4844},
support = {//Leona M. and Harry B. Helmsley Charitable Trust/ ; },
abstract = {BACKGROUND: Biomarkers are needed to predict treatment response and guide therapeutic decisions in Crohn disease (CD). We aimed to develop and validate a multi-omics machine learning (ML) model to predict response to nutritional therapy in pediatric CD.

METHODS: Treatment-naive children with newly diagnosed CD who were initiating exclusive enteral nutrition (EEN) were prospectively enrolled in this study. Metabolomics and lipidomics were measured in the serum and stool, as well as the fecal microbiome. Following feature selection via minimum redundancy maximum relevance, random-forest models were constructed for single- and multi-omics and performances were evaluated. The models were externally validated in an independent prospective cohort of treatment-naive children and young adults with CD treated with EEN.

RESULTS: The discovery cohort consisted of 50 children (mean ± SD age 14.3 ± 2.7 years), of whom 34 (68%) responded to EEN. Combining complementary signals from host metabolism, gut microbiota, and lipid profiles from serum and stool in a multi-omics ML model yielded a model for predicting treatment response (training accuracy 94%; 95% CI, 82%-100%). Key predictive features included serum metabolites (2-hydroxyglutaric acid, Cer[d18:0/22:0], and HexCer[d18:1/d26:1]), fecal metabolites (3-methyladipic acid, DG[16:0 20:0], PC aa C42:2), and microbial taxa (family Bifidobacteriaceae and genus CAG-56). The validation cohort consisted of 21 patients of whom 12 (57%) responded to EEN. The multi-omics model performance achieved an area under the receiver operating characteristic curve (AUROC) of 0.81 (95% CI, 0.6-1.0). Clinical and endoscopic features did not improve the predictive ability of the model.

CONCLUSION: As a proof-of-concept, we showed that integrated multi-omics ML models can predict EEN response in pediatric CD patients, supporting their potential use in precision nutrition and personalized care strategies.},
}

@article {pmid42086392,
year = {2026},
author = {Fan, J and Ye, Y and Xia, W},
title = {Comment on: "Intratumoral microbiome composition and its role in tumor recurrence in primary liver cancer".},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.04.114},
pmid = {42086392},
issn = {0929-6646},
}

@article {pmid42086396,
year = {2026},
author = {Zhang, J and Yang, B and Martin, FM},
title = {Harnessing microbiomes to redefine medicinal plant agriculture.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.04.007},
pmid = {42086396},
issn = {1878-4380},
abstract = {Medicinal plants link agriculture, ecosystem health, and human therapeutics, with bioactive compound profiles providing a direct and economically meaningful readout of microbiome function. Although microbial inoculation can enhance pharmacologically relevant metabolites under controlled conditions, these effects are context dependent and rarely reproducible in the field. This efficacy gap reflects three ecological constraints: introduced microbes are excluded by resident communities, environmental variation overrides laboratory-optimised functions, and inoculants fail to persist without mutualistic feedback. Addressing these barriers requires shifting from disposable inputs to microbiome stewardship: rewilding beneficial communities, designing climate-adapted consortia, and managing soil as living infrastructure. Whether such stewardship produces measurably different bioactive profiles and therapeutic outcomes under field conditions remains the empirical question on which its One Health rationale ultimately depends.},
}

@article {pmid42086397,
year = {2026},
author = {Cheng, Y and Wang, Y and Luo, T and Guo, L},
title = {Challenges and future directions in AI-driven biomaterials for microbiome-associated oral infectious diseases: A systematic review.},
journal = {Dental materials : official publication of the Academy of Dental Materials},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.dental.2026.04.025},
pmid = {42086397},
issn = {1879-0097},
abstract = {Oral biofilm-induced antimicrobial resistance is the core pathogenic mechanism of microbiome-associated oral infectious diseases (dental caries, periodontitis, peri-implantitis, and endodontic infection). Traditional therapies and biomaterials are limited by poor biofilm penetration, drug resistance induction, single functionality, and inadequate adaptation to dynamic oral microenvironmental changes (e.g., pH fluctuations, salivary rinsing, masticatory stimulation). Artificial intelligence (AI) has transformed the field by integrating materials science, microbiology, and stomatology data. Via machine learning, deep learning, and multi-physics simulation, AI optimizes biomaterial physicochemical properties, decodes microenvironmental signals, constructs precise sensing-response loops, and supports the full chain of material design, performance prediction, and action simulation, advancing treatment from empirical intervention to precision regulation. This systematic review retrieved literature from PubMed, Embase, and Web of Science (January 2016-January 2026) using keywords across three dimensions: AI, biomaterials, and oral microbiome. Following inclusion/exclusion criteria, 99 articles were included. It elaborates on five core mechanisms of AI-driven oral biomaterials (precise oral microbiome analysis, targeted material design/optimization, performance prediction/simulation, targeted delivery/intervention, effect evaluation/dynamic regulation), analyzes their applications in microbiome-targeted biomaterial research and development (R&D) and clinical practice for the four major oral infectious diseases, addresses technical bottlenecks (insufficient targeting specificity and precision of biomaterials, poor stability and durability in complex oral microenvironments, inadequate biofilm disruption capacity, and clinical translation obstacles), and proposes future directions (multimodal design to enhance targeting specificity, structural and component optimization to improve stability/durability, development of multi-mechanism synergistic biofilm disruption strategies, strengthening translational research for clinical application, and deep integration of AI in the full chain of biomaterial R&D). This work provides comprehensive theoretical and practical support for the R&D, optimization, and clinical translation of AI-driven microbiome-targeted oral biomaterials.},
}

@article {pmid42086572,
year = {2026},
author = {Gracie, R and Wiedenmann, J and Lam, P and Sweet, M and D'Angelo, C},
title = {Breakdown of microbial networks links nutrient stress and reef coral disease.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42086572},
issn = {2041-1723},
support = {522271101//Leverhulme Trust/ ; INSPIRE DTP//RCUK | Natural Environment Research Council (NERC)/ ; },
mesh = {Animals ; *Coral Reefs ; *Anthozoa/microbiology ; Nitrogen/metabolism/analysis ; *Microbiota/physiology ; Seawater/chemistry/microbiology ; Phosphorus/metabolism/analysis ; Cyanobacteria/isolation & purification/metabolism ; Symbiosis ; Stress, Physiological ; Nutrients/metabolism ; Ecosystem ; },
abstract = {Coral diseases are increasing in prevalence, accelerating the global decline of tropical reefs, which threatens over 25% of marine biodiversity and vital ecosystem services for human societies. While outbreaks are frequently linked to environmental change, including heat stress, sedimentation, and reduced water quality, the mechanisms by which such factors promote disease remain poorly understood. Here we show that nutrient stress, caused by skewed seawater nitrogen-to-phosphorus (N:P) stoichiometry, promotes the onset of Black Band Disease (BBD), a common and easily recognisable syndrome that affects corals around the globe. Using Turbinaria reniformis as a model system, controlled laboratory experiments demonstrate that skewed N:P ratios disrupt the functional integrity of coral-associated microbial networks while favouring opportunists that exploit dysfunctional host-symbiont interactions. Disease lesion-associated microbial mats are dominated by cyanobacteria and include sulphur-metabolising bacteria, hallmarks of natural BBD communities. Strikingly, similar cyanobacterial taxa are also detected in the visually healthy coral tissue ahead of the expanding lesions, suggesting an opportunistic recruitment of disease-associated members from the resident microbiome. Global analyses of BBD outbreaks reveal that over 88% occurred in regions with skewed N:P ratios, compared with only 16% that were linked to prior heat stress. Together, our findings identify nutrient-driven microbiome destabilisation as a key pathway to coral disease, reinforcing nutrient management as a major lever for reef conservation and restoration practice.},
}

Animals
*Coral Reefs
*Anthozoa/microbiology
Nitrogen/metabolism/analysis
*Microbiota/physiology
Seawater/chemistry/microbiology
Phosphorus/metabolism/analysis
Cyanobacteria/isolation & purification/metabolism
Symbiosis
Stress, Physiological
Nutrients/metabolism
Ecosystem