@article {pmid42885922,
year = {2026},
author = {Hussain, A and Bhardwaj, P and Ray, AK and Singh, A and Sett, A and Pathania, R},
title = {Acetate modulates host physiology and bacterial energetics to improve antibiotic efficacy during obesity-associated infection.},
journal = {mBio},
volume = {},
number = {},
pages = {e0163026},
doi = {10.1128/mbio.01630-26},
pmid = {42885922},
issn = {2150-7511},
abstract = {UNLABELLED: Antibiotic efficacy is conventionally attributed to the susceptibility of the infecting pathogen. However, obese patients experience disproportionately poor infection outcomes despite receiving antibiotics to which pathogens remain genetically susceptible. These observations suggest that host-associated factors can influence treatment outcomes independently of the bacterial genotype, although the underlying mechanisms remain poorly understood. Using a mechanistic comparison of diet-induced obese and healthy mice infected with Acinetobacter baumannii, we demonstrate that the effect of antibiotics is not solely a property of the pathogen but can be governed by a gut microbiota-derived metabolite acting on both host immunity and bacterial physiology. We identify obesity-associated acetate depletion as a key driver of antibiotic treatment failure, linking gut microbial metabolism to antibiotic activity during infection. We observed that this depletion impaired innate immune activation, reducing cytokine responses and neutrophil-mediated bacterial clearance. Under these conditions, A. baumannii displayed enhanced tolerance to bactericidal antibiotics, particularly tobramycin. Given these findings, we investigated whether acetate could be leveraged therapeutically to restore antibiotic efficacy. We observed that oral acetate supplementation remodeled the dysbiotic microbiome, whereas systemic acetate restored innate immune competence and neutrophil-mediated bacterial clearance. Most importantly, acetate reversed antibiotic tolerance and restored aminoglycoside killing by directly sensitizing host-induced tolerant bacterial populations. Mechanistically, acetate directly reprogrammed bacterial physiology to enhance aminoglycoside-mediated killing. Combined acetate-tobramycin treatment resulted in eradication of tolerant populations and markedly improved bacterial clearance in vivo. Our findings establish a mechanistic link between host metabolic state and antibiotic efficacy and identify acetate as a therapeutic intervention for obesity-associated gram-negative infections.

IMPORTANCE: Antibiotic treatment failure in obese patients remains poorly understood and therapeutically unaddressed. This study reveals that host metabolic state can control antibiotic response through a gut microbiota-derived metabolite that acts on both host defense and bacterial physiology. We identify obesity-driven depletion of microbiota-derived acetate as a previously unrecognized determinant of antibiotic failure, operating independently of bacterial resistance. By simultaneously restoring gut microbial balance, rescuing impaired innate immunity, and directly sensitizing pathogens to aminoglycoside killing through bacterial membrane alteration, acetate supplementation addresses the host-pathogen-microbiome axis through a single intervention. Given its established clinical safety, acetate represents a compelling combination therapy alongside aminoglycosides in obesity-associated gram-negative infections in a population for which host-directed treatment strategies are currently limited.},
}

@article {pmid42885945,
year = {2026},
author = {Shremo Msdi, A and Begum, K and Hu, C and Shaw, N and Mai, A and Alam, MJ and Bassères, E and Eubank, T and Yu, XY and Mortin, LI and Silverman, MH and Garey, KW},
title = {The effects of novel oral preclinical PolC inhibitor antibiotic candidates on the gut microbiome in a murine thigh infection model.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0114326},
doi = {10.1128/spectrum.01143-26},
pmid = {42885945},
issn = {2165-0497},
abstract = {UNLABELLED: Antibiotics can negatively affect gut microbiome composition and function. However, preclinical evaluations of antibiotic effects on the microbiome are rarely undertaken. The purpose of this study was to characterize pharmacokinetics and metagenomic profiles of PolC inhibitor compounds compared to linezolid in a neutropenic murine thigh infection model. Neutropenic mice thighs were inoculated with methicillin-resistant Staphylococcus aureus (MRSA) and dosed orally starting 1 h later with ACX-728, ACX-801, ACX-978, or linezolid. Untreated control mice were euthanized at 1 h for baseline data, and a second untreated group were euthanized at 24 h after the start of dosing, when all remaining mice were euthanized. At euthanasia, thigh muscles were excised for MRSA quantification, and fecal pellets, colon tissue, and plasma samples were collected for drug concentration and microbiome analyses. All PolC inhibitors were detectable in plasma and feces at 25 h. Compared with linezolid, PolC inhibitors maintained greater gut microbial richness and diversity in this acute murine infection model. PolC-treated samples preserved overall community structure and Bacteroidota dominance, whereas linezolid induced marked disruption, with secondary expansion of Pseudomonadota, primarily Escherichia coli. Microbial pathway analysis showed preservation of community-level metabolic function for PolC inhibitors but marked disruption by linezolid. Compared to controls, linezolid produced a 4.4 log reduction in MRSA colony-forming unit per gram, while the PolC inhibitors produced a mean log reduction of 0.4-2.5 per group. In these exploratory studies, PolC inhibitor compounds preserved anaerobic community structure and fermentative capacity, whereas linezolid induced depletion of healthy commensals and expansion of aerotolerant taxa. These findings highlight the importance of microbiome-informed antibiotic evaluation in preclinical studies. Larger preclinical and clinical studies are warranted to confirm these findings.

IMPORTANCE: This study evaluated the class effect of PolC inhibitors on the microbiome as part of the preclinical development plan for systemic PolC inhibitors. Similar to the non-absorbable antibiotic, ibezapolstat, a narrow effect on the microbiome was observed with these novel compounds.},
}

@article {pmid42886012,
year = {2026},
author = {Gao, L and Sun, X and Wang, X and Wang, S and Du, H and Ma, M},
title = {Integrated multi-omics analysis of root transcriptomic, metabolomic, and bacterial-community responses associated with rhizobial inoculation and cadmium exposure in Robinia pseudoacacia.},
journal = {Tree physiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/treephys/tpag153},
pmid = {42886012},
issn = {1758-4469},
abstract = {Cadmium (Cd) contamination threatens soil ecosystems and food security. Robinia pseudoacacia is a potential candidate for phytoremediation, but the molecular responses and root-associated microbial responses accompanying rhizobial symbiosis under Cd exposure remain incompletely understood. We integrated root transcriptomic, internal-root metabolomic, and 16S rRNA gene sequencing data to characterize responses to Cd exposure and rhizobial inoculation in SX, the high shoot-Cd accumulator, and HB, the low shoot-Cd accumulator. SX and HB exhibited distinct transcriptional patterns and exploratory candidate-metabolite profiles. In SX, the transcriptional responses were associated with the greater shoot Cd translocation reported previously for this genotype. In HB, rhizobial inoculation under Cd exposure was associated with broader changes in candidate metal-transport and compartmentalization genes, consistent with its previously reported greater root Cd retention. Rhizobial inoculation was also associated with higher candidate abundances of leucine, trehalose, palmitic acid, thymine, and pantothenates in HB, whereas inoculated SX showed higher candidate abundances of leucine and isoleucine but lower internal L-malic acid. Cd exposure, rhizobial inoculation, and root compartment were associated with variation in bacterial community composition, including abundance patterns involving Pseudomonas, Devosia, and Rhizobium. Exploratory Spearman correlation analyses revealed compartment-specific patterns of covariation between candidate metabolites and bacterial genera; however, no metabolite-genus association remained statistically significant after Benjamini-Hochberg correction in the rhizoplane, endosphere, or rhizosphere. None of the compartment-specific Procrustes tests indicated significant overall concordance between bacterial community composition and root-metabolite profiles. Collectively, these findings identify candidate genes, metabolites, and bacterial taxa and provide testable hypotheses that could inform future genotype selection and microbiome-assisted phytoremediation strategies.},
}

@article {pmid42886076,
year = {2026},
author = {Lynch, VG and Timilsina, R and Clark, C and Olson, C and Ruth, E and El-Hadedy, DE and Lee, A},
title = {Parental Care Modulates Early-Life Oral Microbiome Assembly and Immune Ontogeny in Wild Birds.},
journal = {Integrative and comparative biology},
volume = {},
number = {},
pages = {},
doi = {10.1093/icb/icag167},
pmid = {42886076},
issn = {1557-7023},
abstract = {A young bird meets its first microbes before its immune system is finished being built. By early-life microbiome dynamics we mean the changes in which microbes arrive, persist, and are lost over the first days and weeks of life. When we understand those dynamics, we can tell how much of a wild bird's microbiome its parents hand to it and how much its own maturing mucosa selects. We can then ask how that first community trains the immune system that will later regulate it. Developing birds offer a model for this work because rapid shifts along avian host developmental trajectories continually reshape the physiological and biochemical landscape of the oral mucosa. In turn, these dynamic transitions modulate local selective pressures, dictating which microbial lineages persist, interact, and establish long-term residence. The avian oral cavity thus serves as a tractable experimental interface for studying host-symbiont dynamics within a coupled holobiont framework. Tracking primary microbial colonizers, such as bacteria and archaea, alongside key host developmental milestones, such as the onset of endothermy in altricial nestlings, which alters physiological profiles like temperature and pH, enables us to directly observe ontogenetic microbial succession and gain insight into the ecological mechanisms governing early-life community assembly. Evaluating the holobiont as a unified unit of selection provides a mechanistic framework for understanding ontogenetic succession-one that can be tested against alternative assembly models such as host-genetic control, diet-driven replacement, and stochastic colonization. Although current evidence confirms that the oral microbiome serves as a distinct ecological record of environmental exposure and anatomical site, its ability to actively shape host immune phenotypes, stress responses, or overall fitness demands rigorous experimental testing. The nestling oral cavity provides a highly accessible surface for longitudinal research, where the "host clock" of mucosal immune maturation and the "microbial clock" of community assembly run in tandem. Validating or refuting this framework will require within-individual longitudinal sampling alongside targeted manipulations of mucosal immunity (e.g., IgA), advancing the field toward a mechanistic grasp of how early environmental exposures establish lasting biological organization.},
}

@article {pmid42886170,
year = {2026},
author = {Park, K and Joo, MK and Lee, IH and Woo, JH and Park, HS and Kong, CH and Jung, SY and Woo, SY and Kim, JY and Park, HJ and Kim, JW and Kim, DH and Ryu, JH and Choi, JH},
title = {Schizophrenia-associated gut microbiota are linked to reduced colonic PRODH expression and behavioral changes in mice.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748081},
doi = {10.1080/19490976.2026.2748081},
pmid = {42886170},
issn = {1949-0984},
mesh = {Animals ; Male ; *Proline Oxidase/genetics/metabolism ; Mice ; Mice, Inbred C57BL ; *Schizophrenia/microbiology/physiopathology ; *Gastrointestinal Microbiome ; *Colon/microbiology/enzymology ; Humans ; Fecal Microbiota Transplantation ; Bacteria/classification/genetics/isolation & purification/enzymology ; Behavior, Animal ; Proline/blood ; },
abstract = {Schizophrenia (SCZ) is a chronic neuropsychiatric disorder whose biological basis remains incompletely understood. Growing evidence implicates the gut-brain axis in SCZ, but the host pathways through which disease-associated microbiota may influence behavior remain unclear. Here, we examined whether the gut microbiota from patients with SCZ is associated with behavioral and metabolic alterations in male C57BL/6N mice. Fecal microbiota transplantation (FMT) from patients with SCZ was associated with impaired short-term recognition memory, reduced social novelty preference, and decreased prepulse inhibition in recipient mice. Transcriptomic profiling of colonic tissue identified reduced expression of Prodh, which encodes proline dehydrogenase (PRODH), together with elevated plasma proline levels. Comparative microbiome analyses identified a five-species candidate consortium associated with the SCZ donor microbiome - Escherichia fergusonii, Shigella sonnei, Morganella morganii, Citrobacter freundii, and Enterococcus faecalis. Oral administration of this five-species mixture (5-SM) was associated with similar behavioral changes, reduced colonic PRODH expression, and hyperprolinemia in mice. Together, these findings support a possible association between schizophrenia-associated changes in the gut microbiota, altered intestinal proline metabolism, and behavioral changes in mice.},
}

Animals
Male
*Proline Oxidase/genetics/metabolism
Mice
Mice, Inbred C57BL
*Schizophrenia/microbiology/physiopathology
*Gastrointestinal Microbiome
*Colon/microbiology/enzymology
Humans
Fecal Microbiota Transplantation
Bacteria/classification/genetics/isolation & purification/enzymology
Behavior, Animal
Proline/blood

@article {pmid42886419,
year = {2026},
author = {Bagul, SY and Sarkar, R and Suthar, MK and Kumar, V and S, S and Rana, VS and Sircar, D and Reddy, NRR},
title = {Culturomics and amplicon-based insights into the endophytic microbiome of Kalmegh (Andrographis paniculata (Burm.f.) Nees) and its implications in plant growth promotion.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {11},
pages = {},
pmid = {42886419},
issn = {1573-0972},
support = {NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR - National Agricultural Science Fund/ ; (NASF/MA-10007/2023-24//ICAR-National Agricultural Science Fund (NASF)/ ; },
mesh = {*Endophytes/classification/isolation & purification/genetics/metabolism ; *Bacteria/classification/isolation & purification/genetics/metabolism ; *Microbiota/genetics ; *Andrographis/microbiology/growth & development ; Diterpenes/metabolism ; Plant Leaves/microbiology/chemistry ; Plants, Medicinal/microbiology/growth & development ; Plant Development ; Metagenomics ; Phylogeny ; Plant Stems/microbiology ; Andrographis paniculata ; Plant Extracts ; },
abstract = {Leaf and stem endophytic microorganisms play an important role in plant physiology and secondary metabolite biosynthesis of plants, particularly in medicinal plants. Kalmegh (Andrographis paniculata (Burm.f.) Nees) is an important medicinal plant with liver-protective, anti-inflammatory, ovicidal, larvicidal, and anti-urolithatic properties. The medicinal activities are due to presence of andrographolides. This study investigated the culture-independent diversity of endophytic bacteria associated with Kalmegh at nursery, vegetative, and flowering stages using a metagenomic approach. The results revealed that Sphingomonas was the dominant bacterial genus during nursery and vegetative stages, whereas Halobacterium predominated during the flowering stage. Microbial abundance was highest in the nursery stage, followed by flowering and vegetative stages. Functional analysis showed that flowering stage endophytes were enriched with specialized carbon metabolism and aromatic compound degradation pathways, potentially influencing andrographolide biosynthesis. Chemical analysis supported these findings, showing the highest andrographolide content in leaves during flowering (3.1%). Gene expression analysis further demonstrated that increased andrographolide accumulation was associated with upregulation of methyl erythritol phosphate pathway (MEP) pathway and diterpene biosynthetic genes. Bacterial endophytes isolated from flowering-stage leaves exhibited plant growth-promotion, antifungal, and seed germination-enhancing activities. In vitro assays against Fusarium wilt and Rhizoctonia disease showed that Bacillus cereus strains KL11, KL12, and KL5 inhibited pathogen growth by 60-65%. Biopriming with strains KL3 and KL5 of Bacillus cereus improved seed germination and plant growth. Pot trials with Micrococcus luteus KES1 increased herbage yield, plant height, and andrographolide content by 43%. These findings highlight the potential of leaf and stem endophytes for sustainable improvement of Kalmegh productivity and andrographolide content in the plant.},
}

*Endophytes/classification/isolation & purification/genetics/metabolism
*Bacteria/classification/isolation & purification/genetics/metabolism
*Microbiota/genetics
*Andrographis/microbiology/growth & development
Diterpenes/metabolism
Plant Leaves/microbiology/chemistry
Plants, Medicinal/microbiology/growth & development
Plant Development
Metagenomics
Phylogeny
Plant Stems/microbiology
Andrographis paniculata
Plant Extracts

@article {pmid42886462,
year = {2026},
author = {Chandran, S and Ramseena, MKF and Abdulaziz, A},
title = {Engineering the gut microbiome with metal-resistant bacteria could protect Artemia nauplii from cadmium toxicity.},
journal = {Biometals : an international journal on the role of metal ions in biology, biochemistry, and medicine},
volume = {},
number = {},
pages = {},
pmid = {42886462},
issn = {1572-8773},
support = {FTC090603//Council of Science and Industrial Research , Government of India/ ; },
abstract = {Metal pollution and emerging contaminants, such as metal nanoparticles, are increasingly found in estuarine and coastal environments. These pollutants pose significant risks to aquatic life and human health and may affect food security. This study evaluates host-associated microbiome engineering as a biological method to reduce cadmium toxicity in an aquatic invertebrate model. We designed a consortium of metal-resistant bacteria through systematic screening and exclusion of isolates from various marine ecosystems. This process resulted in a functionally compatible consortium comprising Bacillus altitudinis, Lacticaseibacillus rhamnosus, Bacillus cereus and Weissella cibaria. The consortium members tolerated up to 1 mM CdCl2 independent of active efflux mechanisms, bile salts, and gastric juices, and formed stable biofilms. The strains did not display antagonistic behaviour towards each other and effectively inhibited pathogenic Vibrio spp. from both environmental and clinical sources. Scanning electron microscopy (SEM) and Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) analyses confirmed the maintenance of cell wall integrity under cadmium stress and the presence of bioaccumulation factors greater than one. Artemia nauplii pre-colonized with the bacterial consortium demonstrated a 33.6% increase in survival during acute (1.5 mM) cadmium exposure compared to untreated controls. These findings suggest that microbiome-based interventions can enhance host tolerance to metal pollution and represent a promising biological approach to mitigating the ecological impacts of metal contamination in aquatic environments.},
}

@article {pmid42886508,
year = {2026},
author = {Chong, L and Rampersaud, H and Rao, A and Gujare, I and Makhijani, A and Kim, D and Levy, E and Beatty, B and Kobayashi, S},
title = {Gut-heart-kidney communication in cardiovascular disease: from a single-metabolite hypothesis to a context-dependent metabolite network.},
journal = {American journal of physiology. Heart and circulatory physiology},
volume = {331},
number = {5},
pages = {H1515-H1529},
doi = {10.1152/ajpheart.00584.2026},
pmid = {42886508},
issn = {1522-1539},
mesh = {Humans ; Animals ; *Cardiovascular Diseases/metabolism/microbiology/physiopathology ; *Gastrointestinal Microbiome ; Methylamines/metabolism ; *Kidney/metabolism/physiopathology ; *Heart/physiopathology ; },
abstract = {Gut microbiota-derived metabolites are increasingly recognized as key mediators of interorgan communication in cardiovascular disease. However, the field has often relied on a single-metabolite hypothesis, particularly centered on trimethylamine N-oxide (TMAO), which does not fully capture the complexity of host-microbe-organ interactions. In this review, we argue that cardiovascular risk is better understood as a network of interacting gut-derived molecules, in which TMAO functions as a node within a broader system that includes phenylacetylglutamine, indole-related metabolites, short-chain fatty acids, bile acids, and lipopolysaccharide. Within this framework, the TMAO two-hit model, in which pre-existing organ vulnerability (first hit) is exacerbated by metabolite elevations (second hit), exemplifies context-dependent pathogenicity, particularly in chronic kidney disease or other pre-existing cardiometabolic vulnerabilities. We further discuss how this network-based view may refine biomarker interpretation, improve patient stratification, and guide the development of biomarker-guided strategies for microbiome-targeted interventions. By reframing gut-derived metabolites as part of an interorgan communication network rather than isolated mediators, this review aims to provide a more integrated translational perspective for cardiovascular pathophysiology and patient stratification.},
}

Humans
Animals
*Cardiovascular Diseases/metabolism/microbiology/physiopathology
*Gastrointestinal Microbiome
Methylamines/metabolism
*Kidney/metabolism/physiopathology
*Heart/physiopathology

@article {pmid42886573,
year = {2026},
author = {Hou, S and Jiang, Y and Zhang, D and Xu, Z and Li, Y and Liu, X and Zhang, H and Zhang, J and Zhai, Q and Zhang, C and Wang, X and Huang, S},
title = {A high-resolution spatial model of the primate gut microbiome defines niche-specific functions and host-adapted microbial metabolism.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748153},
doi = {10.1080/19490976.2026.2748153},
pmid = {42886573},
issn = {1949-0984},
mesh = {Animals ; Humans ; *Macaca mulatta/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Gastrointestinal Tract/microbiology ; Bile Acids and Salts/metabolism ; Metagenomics ; *Host Microbial Interactions ; },
abstract = {The spatial organization of the gastrointestinal microbiome is shaped by strong physicochemical gradients along the gut, yet many region-associated microbial niches remain poorly resolved in humans. Here, we used the rhesus macaque (Macaca mulatta) as a spatially resolved primate model to profile 148 luminal and mucosal samples across the gastrointestinal tract using shotgun metagenomics, 2bRAD-M sequencing, and targeted bile acid metabolomics, complemented by comparative human datasets. Microbial communities exhibited strong spatial stratification along the gastrointestinal tract, while host species explained greater variation than anatomical location in our comparative datasets. Despite broad phylum-level similarity between humans and monkeys, substantial divergence emerged at species and functional levels. Monkey-associated Segatella copri encoded expanded carbohydrate-active enzyme (CAZyme) repertoires specialized for degradation of complex plant polysaccharides, consistent with dietary and other host-associated adaptation. Along the gastrointestinal tract, microbial load and diversity followed pronounced spatial gradients, although the low-biomass stomach retained unexpectedly high taxonomic and functional diversity. Mucosal communities largely mirrored luminal microbiota at broad taxonomic scales but exhibited distinct species-level signatures associated with niche-specific functional specialization. The monkey large intestine was further enriched in the immunomodulatory bile acid isoallo-lithocholic acid (isoalloLCA), with candidate biosynthetic genes identified in previously uncharacterized microbial lineages. Together, these findings establish a high-resolution framework of the primate gut microbiome and reveal how spatial organization and host-associated selection shape microbial metabolism and host-microbe interactions relevant to gut health.},
}

Animals
Humans
*Macaca mulatta/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Gastrointestinal Tract/microbiology
Bile Acids and Salts/metabolism
Metagenomics
*Host Microbial Interactions

@article {pmid42886724,
year = {2026},
author = {Ametefe, EN and Saka, D and Anang, JN and Doh, LS and Adjorlolo, LK},
title = {Probiotics as a Strategy for Mitigating Viral Infections in Poultry: Immunomodulatory Mechanisms and Therapeutic Potential.},
journal = {Veterinary medicine and science},
volume = {12},
number = {6},
pages = {e71298},
doi = {10.1002/vms3.71298},
pmid = {42886724},
issn = {2053-1095},
mesh = {Animals ; *Probiotics/pharmacology/therapeutic use ; *Poultry Diseases/virology/prevention & control/immunology ; Newcastle disease virus/physiology/drug effects ; Infectious bronchitis virus/physiology/drug effects ; *Coronavirus Infections/veterinary/immunology/prevention & control/virology ; *Newcastle Disease/prevention & control/immunology ; Poultry ; *Influenza in Birds/prevention & control ; Lactobacillus/chemistry ; Chickens ; *Immunomodulation ; Influenza A virus/physiology ; },
abstract = {Poultry viral infections remain a persistent challenge for the poultry industry, causing significant economic losses and posing potential threats to human health. The escalating frequency of outbreaks involving pathogens, such as infectious bronchitis virus (IBV), Newcastle disease virus (NDV) and avian influenza virus (AIV), underscores the urgent need for effective interventions. Probiotics have gained attention as a promising strategy to combat these viral infections due to their potential in enhancing immune responses and establishing a healthy gut microbiome. A literature search was carried out on Google Scholar, Scopus and PubMed using key search terms, such as 'probiotics', 'Lactobacillus', 'acidophilus', 'poultry', 'viral infections', 'Newcastle Disease Virus (NDV)' and other relevant terms. Inclusion criteria for manuscripts used were based on the relevance to probiotic-based interventions in poultry, the focus on immunological mechanisms and the examination of viral pathogens commonly found in West African poultry farming systems. This review explores the role of probiotics in mitigating the effects of NDV, AIV and IBV in poultry, focusing on their immunomodulatory effects and antiviral mechanisms. Lactobacillus acidophilus, L. casei and L. plantarum have shown an interesting promise in countering NDV infections by modulating immunological parameters and enhancing antibody responses. Similarly, these probiotics have exhibited antiviral activity against AIV, promoting immune activation and reducing viral loads. Additionally, L. acidophilus and L. plantarum have emerged as potential adjuvants for IBV vaccines, improving antibody responses and humoural immunity.},
}

Animals
*Probiotics/pharmacology/therapeutic use
*Poultry Diseases/virology/prevention & control/immunology
Newcastle disease virus/physiology/drug effects
Infectious bronchitis virus/physiology/drug effects
*Coronavirus Infections/veterinary/immunology/prevention & control/virology
*Newcastle Disease/prevention & control/immunology
Poultry
*Influenza in Birds/prevention & control
Lactobacillus/chemistry
Chickens
*Immunomodulation
Influenza A virus/physiology

@article {pmid42886835,
year = {2026},
author = {Barel, O and Arbiv, B and Maslenko, M and Bitton, M and Motro, Y and Moran-Gilad, J},
title = {Multi-site characterization of reproductive tract and gut microbiota in unexplained recurrent pregnancy loss: a case control study.},
journal = {Reproduction & fertility},
volume = {},
number = {},
pages = {},
doi = {10.1530/RAF-26-0095},
pmid = {42886835},
issn = {2633-8386},
abstract = {This cross-sectional case-control study aimed to characterize microbial communities across multiple anatomical sites in women with unexplained recurrent pregnancy loss compared with healthy controls. Forty women aged 18-40 years, including 20 with unexplained recurrent pregnancy loss and 20 healthy controls, were enrolled at Samson Assuta University Hospital in Ashdod, Israel. Swab samples from the cervix, posterior fornix, lower vagina, and feces were analyzed using 16S ribosomal ribonucleic acid amplicon sequencing. Microbial community composition, diversity, differences in taxon abundance, and concordance between anatomical sites were assessed. Microbial communities were dominated by Lactobacillus across all reproductive-tract sites in both groups. Faith's phylogenetic diversity was significantly higher in women with recurrent pregnancy loss in the cervix (P=0.0139) and posterior fornix (P=0.0492), whereas Shannon diversity did not differ between groups. Beta-diversity analysis revealed significant compositional separation at the posterior fornix (R2=0.104, P=0.029). The Lactobacillus to Bifidobacterium log-ratio was significantly lower in women with recurrent pregnancy loss in the posterior fornix (P=0.037), with similar trends at other reproductive-tract sites. No individual taxa reached significance after multiple-testing correction. Microbial communities showed strong concordance among reproductive-tract sites and modestly greater gut-genital concordance in women with recurrent pregnancy loss. These findings suggest that unexplained recurrent pregnancy loss is associated with subtle, site-specific microbial differences, with the posterior fornix showing the clearest differences between groups.},
}

@article {pmid42887114,
year = {2026},
author = {Jin, R and Zhou, Q and Deng, S and Hu, C and Zhou, Q and Ma, L},
title = {Phosphate rock drives greater arsenic accumulation in Pteris vittata than calcium carbonate by enhancing arsenic metabolism and reshaping rhizosphere microbiome.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143917},
doi = {10.1016/j.jhazmat.2026.143917},
pmid = {42887114},
issn = {1873-3336},
abstract = {Poorly-soluble phosphate rock (PR) and CaCO3 can enhance arsenic accumulation in calcicolous As-hyperaccumulator Pteris vittata, but their mechanisms under soil conditions remain unclear. P. vittata was grown for two months in As-contaminated soil (100 mg kg[-1]) receiving 2.0 g kg[-1] Ca as PR, CaCO3, or soluble CaCl2. Plant nutrients, rhizosphere chemistry and bacterial communities, and As-metabolism genes were examined. Compared with CaCO3, PR increased frond As and P by 35% and 28% to 3128 and 3158 mg kg[-1], while CaCO3 produced slightly greater biomass and 10-15% higher rhizosphere available As and P. PR upregulated P-transporter PvPht1;3, arsenate reductase PvHAC2, and arsenite antiporters PvACR3 and PvACR3;3 by 2.0-2.3 fold, whereas CaCO3 induced PvPht1;3, PvPTB1;2, and PvACR3;1/3;2 by 1.7-3.3 fold relative to the soil control. PR retained a more diverse bacterial community (Shannon: 4.20) containing taxa associated with P cycling and As tolerance, whereas CaCO3 showed lower diversity (3.76) under elevated pH. These findings link superior As accumulation under PR to P acquisition, distinct As-metabolism transcriptional responses, and rhizosphere restructuring, providing a mechanistic basis for selecting PR to enhance As accumulation during phytoremediation of As-contaminated soils.},
}

@article {pmid42887214,
year = {2026},
author = {Méndez, JO and Canedo-Marroquín, G and Brinkac Leone, L and Greco, C and Nelson, K and Inostroza Silva, C},
title = {Oral microbiome profiles in a RUT-confirmed gastric H. pylori-positive cohort: A retrospective pilot comparison of specimen-processing workflows.},
journal = {Archives of oral biology},
volume = {192},
number = {},
pages = {106774},
doi = {10.1016/j.archoralbio.2026.106774},
pmid = {42887214},
issn = {1879-1506},
abstract = {OBJECTIVE: To characterize oral microbial profiles in a rapid urease test (RUT)-confirmed gastric Helicobacter pylori-positive cohort and descriptively compare oral specimen-processing workflows.

DESIGN: Archived oral specimens collected during 2015-2016 from adults undergoing diagnostic upper gastrointestinal endoscopy were retrospectively analyzed. Gastric H. pylori status was confirmed by RUT of antral biopsies. The microbiome dataset comprised 32 DNA preparations from 18 RUT-positive participants: 11 buccal-NucleoSpin, 11 saliva-NucleoSpin, and 10 saliva-PowerSoil preparations. Buccal- and saliva-NucleoSpin samples were paired in 11 participants; three also contributed saliva-PowerSoil preparations. The V4 region of the 16S rRNA gene was sequenced using Illumina MiSeq. Alpha diversity, Bray-Curtis dissimilarity, and taxonomic relative abundances were evaluated using the historical workflow.

RESULTS: Buccal-NucleoSpin and saliva-NucleoSpin preparations showed comparable alpha diversity. Shannon diversity did not differ between buccal and saliva specimens (p = 0.13), including when restricted to paired participants. Historical Bray-Curtis comparisons showed differences between buccal and saliva-derived profiles (p = 0.00572); however, the original multivariate model, permutation structure, effect sizes, and dispersion testing could not be retrospectively verified. Taxonomic findings were therefore interpreted descriptively. Saliva-NucleoSpin profiles showed higher relative representation of Streptococcus and Veillonella, whereas buccal-NucleoSpin profiles showed higher relative representation of Neisseria and Pseudomonas. No Helicobacteriaceae signal remained after filtering.

CONCLUSIONS: Oral microbiome profiles differed among specimen-processing workflows. Buccal-swab and saliva-derived preparations provided complementary representations; however, because specimen type, preservation, and extraction procedures were not fully crossed, their individual contributions could not be separated. Standardized sampling and laboratory procedures are essential for reproducible oral microbiome studies.},
}

@article {pmid42887222,
year = {2026},
author = {Kohda, C and Iyoda, M and Tanaka, K},
title = {Cytomegalovirus latency and reactivation: Epigenetic control and immune-microenvironment crosstalk.},
journal = {Virology},
volume = {625},
number = {},
pages = {111074},
doi = {10.1016/j.virol.2026.111074},
pmid = {42887222},
issn = {1096-0341},
abstract = {Human cytomegalovirus (HCMV) establishes lifelong latency following primary infection and periodically reactivates under conditions of immune perturbation. Although CMV disease has classically been associated with severe immunosuppression, accumulating evidence indicates that viral reactivation also occurs in critically ill patients, during pregnancy, and in conditions characterized by immune remodeling and chronic inflammation. Recent studies have revealed that CMV latency and reactivation are governed not only by host immune surveillance but also by epigenetic regulation of the viral genome, particularly at the major immediate-early promoter (MIEP). Inflammatory cytokines, cellular differentiation, oxidative stress, and immunosenescence contribute to chromatin remodeling and activation of immediate-early gene expression, thereby promoting viral reactivation. In parallel, CMV has evolved sophisticated immune evasion strategies that enable lifelong persistence despite innate and adaptive immune responses. Emerging evidence has shown strong links between gut microbiota and immunological and metabolic pathway regulation both of which could impact on control of viral latency and reactivation. Microbiota-derived short-chain fatty acids (SCFAs), such as butyrate, may influence viral chromatin states through histone deacetylase inhibition, linking microbial metabolism to epigenetic regulation of CMV. This review summarizes current knowledge regarding the molecular mechanisms underlying CMV latency and reactivation and discusses the roles of host immunity, pregnancy-associated immune tolerance, immune reconstitution inflammatory syndrome, immunosenescence, and the gut microbiome in shaping CMV pathobiology. We also highlight unresolved mechanistic questions and future directions for understanding CMV-host-microenvironment interactions.},
}

@article {pmid42887291,
year = {2026},
author = {Perlin, CM and Keingeski, MB and Basso, BS and Mendes, BG and Medeiros, JD and Borges, FM and Schnabl, B and Álvares-da-Silva, MR},
title = {Gut mycobiome in the spectrum of Metabolic-dysfunction Associated Steatotic Liver Disease (MASLD): from MASH to hepatocellular carcinoma.},
journal = {Clinics (Sao Paulo, Brazil)},
volume = {81},
number = {},
pages = {101200},
doi = {10.1016/j.clinsp.2026.101200},
pmid = {42887291},
issn = {1980-5322},
abstract = {UNLABELLED: Gut Microbiome (GM) dysbiosis is associated with the development and progression of Metabolic-dysfunction Associated Steatotic Liver Disease (MASLD) and steatohepatitis (MASH). Human GM contains bacteria, fungi, archaea, and viruses. Gut mycobiome (GMyco) is still poorly studied in patients with MASLD. Herein we investigated GMyco composition at different MASLD stages.

METHODS: 23 patients were recruited: controls (n = 5); MASH (n = 6); cirrhosis (n = 7); and Hepatocellular Carcinoma (HCC) (n = 5). Stool samples were collected and stored in -80 °C for subsequent DNA extraction and profiled by 18S rRNA sequencing. The single sequence variants obtained were inferred with DADA2 and classified with SILVA v138. Diversity metrics (Simpson; Bray-Curtis PERMANOVA) and DESeq2 with BH FDR were used for statistical analysis.

RESULTS: Among 23 participants, 73.9% were women, and the average BMI was 30.7 kg/m[2]. Current alcohol use was reported in 17.4%, and chronic medication use in 56.5% of individuals. MASH patients showed greater gut mycobiota alpha diversity compared with controls (p < 0.05). Controls exhibited higher relative abundance of the phylum Ascomycota, whereas Basidiomycota predominated in MASH. At the family level, Aspergillaceae was more abundant in controls, Malasseziaceae and Sporidiobolaceae in cirrhosis, and Saccharomycetaceae in HCC. Differential abundance analysis identified three ASVs differing between groups, with one ASV (genus Naganishia) homogeneously distributed in MASH and absent in controls.

CONCLUSIONS: The gut mycobiota profile varied across the MASLD spectrum, with stage-specific enrichment of certain taxa despite overall similarity in community structure. Basidiomycetes ‒ notably Malassezia and Naganishia ‒ were more abundant in MASH, while Saccharomyces dominated in advanced stages. These findings suggest that distinct fungal signatures accompany disease progression and may serve as potential biological markers in MASLD.},
}

@article {pmid42887297,
year = {2026},
author = {Mendes-Oliveira, F and Belisário, AR and Martins, ML and Martins, RCR and Franco, LAM and Scaccia, N and Fonseca, JVDS and Moura, ICG and de Souza, VR and Costa, SF and Valença, I and Bolina-Santos, E and Mendes, FG and Moreno, EC and Timponi, A and Coelho Dos Reis, JGA and Martins-Filho, OA and Carneiro-Proietti, AB and Sabino, EC},
title = {Microbial diversity in leg ulcer and skin in Sickle Cell disease.},
journal = {Hematology, transfusion and cell therapy},
volume = {48},
number = {4},
pages = {108550},
doi = {10.1016/j.htct.2026.108550},
pmid = {42887297},
issn = {2531-1387},
abstract = {INTRODUCTION: Leg ulcers are a common, painful, and difficult-to-treat complication of sickle cell disease due to their prolonged healing process. The microbial composition of these wounds remains poorly understood. This study investigated the microbiota diversity in sickle cell disease leg ulcers and associations with laboratory parameters.

METHODS: Samples were collected from leg ulcers, intact skin adjacent to the ulcers, and intact skin from healthy controls. Microbiome profiling was performed by sequencing the V4 region of the 16S ribosomal RNA (rRNA) gene. The laboratory results of patients with sickle cell disease leg ulcers were analyzed alongside the identified taxa using correlation-based analyses.

RESULTS: Microbial diversity was significantly lower in sickle cell disease leg ulcers compared to intact skin. Additionally, leukocytes and mean corpuscular volume were statistically associated with the relative abundance of bacteria of the genera Pseudomonas and Aeromonas. Staphylococcus spp. was the predominant genus identified in leg ulcers and was negatively associated with Pseudomonas spp., reflecting a dysbiotic microbial profile characterized by taxa commonly associated with chronic wounds.

CONCLUSIONS: The observed associations between bacterial taxa and laboratory parameters are exploratory, do not imply causality, and contribute to the characterization of the microbial ecology of sickle cell disease leg ulcers.},
}

@article {pmid42887308,
year = {2026},
author = {Zhang, L and Ye, M and Dong, Y and Yuan, L and Qiu, S and Shao, H and Zhang, D},
title = {Modulation of the gut microbiome and resistome in Taihe Black-Boned Silky Fowls by different dietary selenium forms.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107919},
doi = {10.1016/j.psj.2026.107919},
pmid = {42887308},
issn = {1525-3171},
abstract = {Selenium is a widely utilized supplement in poultry production. Its bioavailability and tissue deposition vary with chemical form and may affect the gut microenvironment. Taihe Black-Boned Silky Fowl (TBSF), a Chinese endemic breed with systemic melanin deposition, exhibit enhanced absorption and enrichment of diverse compounds. As a metalloid, selenium may also promote antimicrobial resistance in microbiomes, including those of the gut. However, its impact on the TBSF gut microbiota and resistome remains unknown. We therefore investigated how selenium chemical form influences the cecal microbiome and resistome. Four dietary treatment groups of TBSF (n = 120 birds per group; 60 males and 60 females) were fed for 80 days: CK (selenium-deficient control), YS (sodium selenite), JS (yeast-derived selenium), and DS (selenomethionine), with measured dietary selenium concentrations of 0.05 ± 0.002, 0.33 ± 0.023, 0.35 ± 0.017, and 0.36 ± 0.042 mg/kg, respectively. We performed metagenomic sequencing analysis to assess alterations in microbial composition and resistome profiles in cecum. Results demonstrated that selenium supplementation significantly modulated cecal microbiota structure in both male and female birds(Bray-Curtis distance-based analysis, Wilcoxon rank-sum test, P < 0.05), with pronounced sex-dependent differences. The relative abundances of three prevalent antibiotic resistance genes (ARGs), bcrA, efrA, and fusA, were significantly elevated in selenium-supplemented groups compared with the CK group (Kruskal-Wallis H test, FDR-adjusted P < 0.05). Selenium supplementation reduced mobile genetic element (MGE) type diversity while increasing overall MGE relative abundance. Transposases and recombinases were the two most abundant MGE-associated functional classes. Mantel correlation analysis revealed strong associations between cecal microbiota composition and both ARG and MGE profiles (r ≥ 0.5, P ≤ 0.001). The sexually dimorphic cecal microbiota composition in TBSF may underlie the observed sex-dependent resistome response: sodium selenite exerted the strongest effect on ARG and MGE enrichment in roosters, whereas yeast-derived selenium induced the strongest effect in hens. Further network analysis revealed that sodium selenite exerted the most pronounced influence on resistome-microbiota co-occurrence patterns. These findings underscored the dual-sided nature of selenium supplementation from the perspective of ARGs, indicating that selenium supplementation may alter the composition of the cecal microbiota, thereby modulating the relative abundance and community structure of ARGs and MGEs in the TBSF cecum. Given selenium's essential role and narrow therapeutic index, its chemical form and dosage must be evidence-based and rigorously optimized to minimize potential unintended contributions to antimicrobial resistance. This represents a potential ecological and antimicrobial resistance concern from a One Health perspective that warrants further investigation.},
}

@article {pmid42887494,
year = {2026},
author = {Jiang, YT and Li, GQ and Zhou, YW and Jiang, ZD and Zhao, YN and Zhang, Y and Yin, XM and Li, S and Tong, H and Feng, LS and Wen, SY and Zhou, XY and Li, RW and Wei, JW and Qiu, JP and Wei, YH and Tan, KQ and Zhang, SX and Zhou, HR and Yang, JQ and Bai, J and Deng, Q and Yang, XG and Yang, XQ and Wang, YS and Wei, XW and Qiu, M and Huang, J and Ma, XL},
title = {Akkermansia muciniphila attenuates macrophage efferocytosis to enhance anti-PD-1 efficacy in microsatellite-stable colorectal cancer.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.09.014},
pmid = {42887494},
issn = {1934-6069},
abstract = {Approximately 85% of colorectal cancers (CRCs) are microsatellite stable (MSS) and thus exhibit intrinsic resistance to anti-programmed death-1 (PD-1) therapy. In this study, we demonstrate that oral administration of Akkermansia muciniphila (Akk) suppresses tumorigenesis and reprograms the tumor microenvironment in MSS CRC mouse models. Akk attenuates macrophage efferocytosis through the TLR2/NF-κB pathway, an effect that leads to the accumulation of apoptotic cancer cells, which activates the cGAS-STING pathway and potentiates type I interferon production. This immunostimulatory cascade activates effector CD8[+] T cells and enhances the response to anti-PD-1 therapy. We conducted a phase 1 trial (NCT06865521) combining Akk probiotics with PD-1 antibody in patients with metastatic MSS CRC after ≥1 prior line of therapy. The combination therapy was safe and achieved an objective response rate of 19%, with responders exhibiting enhanced antitumor immunity. Our multilevel investigation provides a promising strategy to overcome immunotherapy resistance in MSS CRC through targeted modulation of the gut microbiome.},
}

@article {pmid42887877,
year = {2026},
author = {Carson, M and Meadows, V and Nejak-Bowen, K},
title = {Microbiome Targeted Therapies for Primary Sclerosing Cholangitis.},
journal = {Seminars in liver disease},
volume = {},
number = {},
pages = {},
doi = {10.1055/a-2983-7443},
pmid = {42887877},
issn = {1098-8971},
abstract = {Primary sclerosing cholangitis is a rare, progressive cholestatic liver disease of the intrahepatic and extrahepatic bile ducts with poor prognosis. The only life-extending treatment for PSC is liver transplantation, with up to 25% of post-transplant patients developing recurrent disease, highlighting an extrahepatic influence on disease. The gut-liver axis has been widely studied in the development and pathogenesis of PSC, with preclinical and clinical work demonstrating that targeting gut microbiota and its metabolites can elicit therapeutic effects against PSC. This review describes various microbiome-based therapeutics and their effectiveness in treating PSC, including antibiotics, probiotics, fecal microbiota transplantation, and bacteriophages. In conclusion, the use of microbiota-derived metabolites as potential therapeutics is also addressed.},
}

@article {pmid42888046,
year = {2026},
author = {Williams, E and Dyas, R and Colman, K and Kinsella, S and Gwee, A and Lovell, A and Gennery, AR and Slatter, M and Chait-Rubinek, L and Van Der Stoep, E and Lankester, A and Mekelenkamp, H and Gelbart, B and Nicholson, K and McLeman, L and Shanthikumar, S and Clifford, V and Cole, T and Haeusler, GM and Ott de Bruin, LM and Prestidge, T and Nelson, A and Rao, K and Conyers, R and , },
title = {Paediatric haematopoietic stem cell transplantation research priorities: Results from an international multi-stakeholder priority setting partnership.},
journal = {British journal of haematology},
volume = {},
number = {},
pages = {},
doi = {10.1111/bjh.70901},
pmid = {42888046},
issn = {1365-2141},
support = {MRF/2007620//Medical Research Future Fund/ ; },
abstract = {Co-designed research in paediatric HSCT is limited. We sought to determine research priorities which represent the shared priorities of patients, parents, carers and healthcare professionals (HCP) within Australia, New Zealand, the Netherlands and the United Kingdom. An international, multiphase priority-setting methodology was implemented in partnership with the James Lind Alliance and delivered over an 18-month period. Part 1: an international scoping survey asked respondents to submit their research uncertainties related to paediatric HSCT. Part 2: summarising and evidence-checking the submitted uncertainties. Part 3: interim prioritisation survey. Part 4: consensus workshop. In the first international scoping survey, 667 topic ideas were suggested (45% by consumers, 55% by HCP), which were categorised into 80 summary questions. After systematic literature review, 35 summary questions were judged to be true uncertainties (i.e. not answered by existing evidence). These 35 uncertainties were included in a second interim prioritisation survey and completed by 224 participants. From those, a shortlist of 19 questions was drawn. After a multistakeholder workshop, consensus was reached on the top 10 priorities. The PSP identified important research gaps in the management of paediatric HSCT. Priority areas included: implementing personalised medicine approaches, improving immune recovery and adjunct interventions such as exercise, nutrition and microbiome-directed strategies.},
}

@article {pmid42888123,
year = {2026},
author = {Holaman, J and Sills, D and Saumtally, H and Johnson, C and Recto, A and Marsh, R and Prayle, A and Gathercole, K and Monaghan, T and Marciani, L and Spiller, R and Barr, HL and Downey, DG and van der Gast, C and Peckham, D and Stewart, I and Smyth, A},
title = {Distinct gastrointestinal symptom phenotypes in adults with cystic fibrosis are linked to complications and medication use: the GRAMPUS-CF study.},
journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jcf.2026.09.014},
pmid = {42888123},
issn = {1873-5010},
abstract = {BACKGROUND: Gastrointestinal symptoms remain common in adults with cystic fibrosis (CF) despite cystic fibrosis transmembrane conductance regulator modulator use, suggesting persistent and heterogeneous gut dysfunction. This prospective observational study tests the hypothesis that distinct gut symptom phenotypes in CF can be observed and linked to underlying mechanisms.

METHODS: Adults from three UK CF centres completed the Gastrointestinal Symptom Rating Scale, Patient Assessment of Constipation Symptoms and a bowel-habit questionnaire. Latent class analysis using an ordinal logistic model was applied to 36 symptom indicators. Associations between phenotypes and demographic, clinical, and treatment variables were examined using generalised linear models.

RESULTS: Three hundred participants completed questionnaires (54% male; median 31 years). We identified four symptom phenotypes: mild; moderate-constipation predominant; moderate-diarrhoea predominant and severe. The severe phenotype was associated with gastroesophageal reflux (RRR 2.86; 95%CI: 1.30-6.31; p = 0.009), distal intestinal obstruction syndrome (RRR 2.46; 95%CI: 1.04-5.81; p = 0.04), proton pump inhibitor (RRR 3.29; 95%CI 1.39-7.74; p = 0.007), and laxative use (RRR 6.13; 95%CI 2.54-14.84; p < 0.001). CF-related liver disease was associated with both moderate-constipation and diarrhoea phenotypes, respectively (RRR 2.08; 95%CI 1.13-3.81; p = 0.018; RRR 2.11; 95%CI 1.03-4.29; p = 0.04). There was a lower likelihood of long-term oral antibiotic use in the moderate-constipation phenotype (RRR 0.53; 95%CI 0.3-0.92; p = 0.025) and moderate-diarrhoea phenotype (RRR 0.46; 95%CI 0.24-0.91; p = 0.025).

CONCLUSIONS: Four distinct symptom phenotypes were identified, independent of demographics and pancreatic status, but associated with specific complications and medication profiles. These phenotypes provide a framework for mechanistic studies within the GRAMPUS-CF cohort and precision management of CF-related gut disease.},
}

@article {pmid42888205,
year = {2026},
author = {Hoozemans, JB and de Jonge, PA and Guman, MSS and Haal, S and Aydin, Ö and Meijnikman, AS and Bäckhed, F and de Brauw, M and Acherman, YIZ and Nieuwdorp, M and Groen, AK and Gerdes, VEA},
title = {Understanding pathophysiology of gallstone disease: a multi-omic analysis focused on adult women with obesity.},
journal = {International journal of obesity (2005)},
volume = {},
number = {},
pages = {},
pmid = {42888205},
issn = {1476-5497},
abstract = {BACKGROUND: Gallstone disease has a complex, multifactorial pathophysiology. Both the gut microbiome and the liver have been implicated as potential contributors. Because obesity is associated with alterations in gut microbial composition and is itself a risk factor for gallstone formation, we investigated the relative roles of the gut microbiome, the liver, and adipose tissue in gallstone disease in female patients with obesity.

METHODS: From the BARIA cohort, 108 consecutive female patients with obesity were included, of whom at baseline 39 had ultrasound proven gallstones (cases), whereas 69 did not have gallstones (controls). Fecal shotgun metagenomics, untargeted fasting plasma metabolomic analysis, and bulkRNAseq transcriptome analyses of liver, visceral (VAT), and subcutaneous (SAT) biopsies (taken during surgery) were analyzed.

RESULTS: Especially VAT showed differences in expression of 57 genes, whereas liver gene expression revealed differences only after secondary analysis. In contrast to other publications, in liver "classic" ABC transporter gallstone genes were not identified in this cohort. Instead, the cholesterol transporter ABCG1 emerged, and expression was decreased in patients with gallstone disease. Plasma metabolomic profiling demonstrated increased levels of primary and secondary bile acids in the gallstone group. In contrast, gut microbiome differences between groups were limited.

CONCLUSIONS: This integrated multi-omics analysis suggests that visceral adipose tissue may play a more prominent role in gallstone disease pathophysiology in women with obesity than previously appreciated. The observed selective molecular alterations and persistent bile acid differences highlight the complex metabolic interplay underlying gallstone formation and provide insight into tissue-specific mechanisms associated with obesity-related gallstone disease.},
}

@article {pmid42888274,
year = {2026},
author = {Zhou, Y and Ge, Y and Liu, K and Liu, H and Dong, Z},
title = {From HPV infection to cervical precancer: Molecular mechanisms, immune microenvironment and emerging technologies.},
journal = {Cellular and molecular life sciences : CMLS},
volume = {83},
number = {1},
pages = {},
pmid = {42888274},
issn = {1420-9071},
support = {82203343//National Natural Science Foundation of China/ ; 82606606//National Natural Science Foundation of China/ ; BX20220273//National Postdoctoral Program for Innovative Talents/ ; 2022M712874//China Postdoctoral Science Foundation/ ; 252300421123//Outstanding Youth Project of Henan Province Natural Science Foundation/ ; 2025SGAQZ-QN-01//Young Scientist Foundation of State Key Laboratory of Metabolic Dysregulation & Prevention and Treatment of Esophageal Cancer/ ; 262300422369//Natural Science Foundation of Henan Province/ ; },
mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/immunology/virology/pathology ; *Papillomavirus Infections/immunology/virology/pathology/complications ; *Tumor Microenvironment/immunology ; *Precancerous Conditions/immunology/virology/pathology ; *Human Papillomavirus Viruses/immunology ; *Uterine Cervical Dysplasia/immunology/pathology/virology ; },
abstract = {Cervical cancer remains a leading cause of cancer-related mortality among women globally, with persistent high-risk human papillomavirus (HPV) infection as the primary etiological factor. Cervical precancerous lesions, including high-grade squamous intraepithelial lesions and adenocarcinoma in situ, represent the critical window for intervention prior to invasive cancer development. However, additional factors such as immunosuppression, smoking, and microbiome composition also play crucial roles in the development of cervical precancerous lesions. While HPV vaccination, screening, and treatment have reduced cancer incidence, these must be complemented by personalized approaches that target the molecular mechanisms driving carcinogenesis. Key dysregulated tumor suppressors (e.g., p16) and signaling pathways (PI3K/AKT/mTOR, Wnt/β-catenin) highlight the need for advanced therapeutic strategies. The immune microenvironment also plays a critical role in cancer progression, suggesting potential for immunotherapy. Promising biomarkers like p16, Ki67, and microRNAs require integration with technologies such as single-cell RNA sequencing and spatial transcriptomics for deeper insights into tumor heterogeneity and microenvironment dynamics. Additionally, while deep learning models hold promise in improving diagnostic accuracy for cervical intraepithelial neoplasia (CIN), challenges such as data variability and interpretability need addressing. In conclusion, incorporating genomics, transcriptomics, immunotherapy, and artificial intelligence will enable more personalized and effective interventions, ultimately reducing the global burden of cervical cancer.},
}

Humans
Female
*Uterine Cervical Neoplasms/immunology/virology/pathology
*Papillomavirus Infections/immunology/virology/pathology/complications
*Tumor Microenvironment/immunology
*Precancerous Conditions/immunology/virology/pathology
*Human Papillomavirus Viruses/immunology
*Uterine Cervical Dysplasia/immunology/pathology/virology

@article {pmid42888447,
year = {2026},
author = {Hashemzadeh, K and Ghamari, M and Deutsch, S and Schwarting, A and Triantafyllias, K},
title = {Exploring gut microbiome dysbiosis in vasculitis in adults: a systematic review.},
journal = {Systematic reviews},
volume = {15},
number = {1},
pages = {},
pmid = {42888447},
issn = {2046-4053},
mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Vasculitis/microbiology ; *Gastrointestinal Microbiome ; Adult ; },
abstract = {BACKGROUND AND AIM: Although studies have confirmed that disruptions in the gut microbiota (dysbiosis) contribute to the development of autoimmune disorders, the precise pathways through which the gut microbiota influences the onset and progression of vasculitis remain largely unknown. In recent years, research has increasingly concentrated on assessing the contribution of the gut microbiota to vasculitis. This systematic study sought to assess the dominant gut microbiota profiles in vasculitis patients and compare them to those of healthy individuals.

METHODS: The Cochrane methodology was used to design and conduct the present systematic review. Relevant articles published up to May 2025 were searched and collected from four electronic databases: PubMed, Scopus, Medline, and Web of Science. The keywords used in the search included "vasculitis," "Takayasu arteritis," "giant cell arteritis," "polyarteritis nodosa," "microscopic polyangiitis," "granulomatosis with polyangiitis," "eosinophilic granulomatosis with polyangiitis," "cryoglobulinemic vasculitis," "IgA vasculitis," "variable vessel vasculitis," "Behçet's disease," and "Cogan's syndrome" alongside phrases like "gut microbiome," "gut microbiota," and "gut flora."

RESULTS: Overall, 12 publications were included in the analysis. Three addressed individuals with Takayasu arteritis (TAK), three investigated ANCA-associated vasculitis (AAV), another three examined Behçet's disease (BD), while one study each pertained to IgA vasculitis (IgAV), Kawasaki disease (KD), and a nonspecific form of vasculitis. The majority of these works observed variations in both α-diversity and β-diversity, as well as in the diversity and richness of the gut microbiota. Additionally, the structure of the microbial communities differed markedly between those with vasculitis and healthy individuals. Notably, Bacteroidetes, Firmicutes, and Proteobacteria-the dominant bacterial phyla in the human gastrointestinal tract-were frequently diminished in affected patients.

CONCLUSION: The occurrence of intestinal microbial imbalance in individuals diagnosed with vasculitis has been validated. As observed in various other autoimmune conditions, the gut microbiota of vasculitis patients is chiefly comprised Bacteroidetes, Firmicutes, Proteobacteria, and Actinobacteria. Disruptions in the microbial ecosystem-mainly typified by diminished diversity and population density-may play a role in triggering and advancing the disease.

This review was not registered.},
}

Humans
*Dysbiosis/microbiology/complications
*Vasculitis/microbiology
*Gastrointestinal Microbiome
Adult

@article {pmid42888449,
year = {2026},
author = {He, P and Zhang, K and Khan, J and Ouyang, H and Hu, S and Qian, S and Shu, B and Li, X and Lin, D},
title = {Metagenomic analysis of developmental-category-associated fungal communities in the gut contents of Achatina fulica, an intermediate host of Angiostrongylus cantonensis.},
journal = {Parasites & vectors},
volume = {19},
number = {1},
pages = {},
pmid = {42888449},
issn = {1756-3305},
support = {18MDZ02//Major Project Cultivation Plan of Xizang Minzu University/ ; XZ202401ZR0017//the Tibet Natural Science Foundation/ ; No. SKXRC2025159//the Youth S&T Talent Support Programme of Guangdong Provincial Association for Science and Technology/ ; 82672963 and 82202560//the National Natural Science Foundation of China/ ; 23360095 and 23360208//College Students' Innovative Entrepreneurial Training Plan Program/ ; },
mesh = {Animals ; Metagenomics ; *Mycobiome ; *Snails/microbiology/parasitology ; *Angiostrongylus cantonensis/physiology ; China ; *Fungi/genetics/classification/isolation & purification ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/microbiology ; },
abstract = {BACKGROUND: The invasive giant African snail (Achatina fulica) poses serious agricultural and ecological threats and serves as an important intermediate host of the zoonotic parasite Angiostrongylus cantonensis, which causes human eosinophilic meningitis. While its gut bacterial microbiome has been extensively characterized, the gut mycobiome remains largely uncharacterized. In particular, variations in gut fungal communities across developmental stages remain unknown, limiting our understanding of the A. fulica gut holobiont.

METHODS: In November 2025, giant African snails were collected from Guangzhou, Guangdong Province, China. Genomic DNA was extracted from the gut contents of the collected snails. Metagenomic sequencing was conducted to characterize variations in the gut mycobiota across different snail sample types.

RESULTS: Metagenomic sequencing of 18 snail gut samples across three developmental stages showed lower fungal alpha diversity in adults than in juveniles, whereas PCoA visualized differences in community composition among developmental categories and PERMANOVA confirmed that these differences were statistically significant. Ascomycota dominated the mycobiome, with developmental-category-associated differences in taxonomic composition. LEfSe and DESeq2 identified differentially abundant taxa associated with developmental categories, while SIMPER analysis identified several taxa contributing to the observed dissimilarity, including Synchytrium taraxaci, Aspergillus flavus and Cladosporium cladosporioides. These taxa are interpreted as contributors to community dissimilarity rather than as causal drivers of developmental-category-associated differences. Co-occurrence networks analysis identified six highly connected taxa (Hanseniaspora uvarum, Apiospora montagnei, Aureobasidium thailandense, Colletotrichum aenigma, Truncatella angustata, and Calonectria ilicicola) within the inferred fungal association network.

CONCLUSIONS: Gut fungal community composition differed significantly among the sampled developmental categories of A. fulica, although the cross-sectional design does not establish that the host development itself causes these differences. The identified developmental-category-associated and highly connected taxa provide a baseline for gut mycobiota ecology and a foundation for future controlled studies investigating their functional roles and potential relevance to A. cantonensis infection.},
}

Animals
Metagenomics
*Mycobiome
*Snails/microbiology/parasitology
*Angiostrongylus cantonensis/physiology
China
*Fungi/genetics/classification/isolation & purification
*Gastrointestinal Microbiome
Gastrointestinal Tract/microbiology

@article {pmid42888465,
year = {2026},
author = {Zhao, N and Zhang, H and Pang, Y and Zhu, L and Liu, Q and Zhang, Z and Shen, L and He, Y and Lin, S},
title = {Intratumoral microbiota in cancer immunotherapy: metabolic-epigenetic crosstalk and engineered bacterial therapeutics.},
journal = {Experimental hematology & oncology},
volume = {15},
number = {1},
pages = {},
pmid = {42888465},
issn = {2162-3619},
support = {202604841398//Beijing Nova Program/ ; 7262174//Beijing Natural Science Foundation/ ; },
abstract = {The intratumoral microbiome critically influences immunotherapy efficacy by modulating the host immune microenvironment and epigenetic landscape through its metabolites. Microbial derived metabolites such as short chain fatty acids, secondary bile acids, trimethylamine N oxide, and tryptophan derivatives reprogram host cell epigenetics via DNA methylation, histone modifications, and non-coding RNAs, thereby shaping anti-tumor immunity and driving either immune activation or resistance. In turn, the hypoxic, acidic, and nutrient deprived tumor microenvironment reshapes microbial composition and metabolism, forming a vicious cycle that further affects therapeutic outcomes. Given these pivotal roles, targeting the intratumoral microbiota has emerged as a promising strategy. Advances in synthetic biology have enabled the development of engineered bacteria as programmable living therapeutics. These engineered strains achieve tumor specific colonization, controlled drug release, and multimodal functions such as cytokine secretion, immune checkpoint blockade, STING pathway activation, and metabolic reprogramming. By enhancing immune checkpoint inhibitor efficacy and synergizing with cell therapies, engineered bacterial therapy represents a highly promising approach to improve immunotherapy efficiency. Despite challenges in clinical translation including heterogeneity, anti-vector immunity, and manufacturing complexity, this strategy offers a new paradigm for precision cancer treatment.},
}

@article {pmid42888565,
year = {2026},
author = {Ping, S and Li, D and Sun, J and Tao, K and Qin, E and Tang, R and Shan, H and Ye, H and He, M},
title = {Causal relationship between oral microbiome, circulating inflammatory proteins and lung cancer: A Mendelian randomization study.},
journal = {Medicine},
volume = {105},
number = {42},
pages = {e51142},
pmid = {42888565},
issn = {1536-5964},
support = {No. 2023ZL183//Traditional Chinese Medicine Science and Technology Planning Project of Zhejiang Province/ ; No. 2024KY1721//Medical and Health Science and Technology Planning Project of Zhejiang Province/ ; No. 2022KY006//Health Science and Technology Planning Project of Shaoxing/ ; },
mesh = {Humans ; *Lung Neoplasms/microbiology/genetics ; Mendelian Randomization Analysis ; *Microbiota ; Genome-Wide Association Study ; *Mouth/microbiology ; Inflammation ; },
abstract = {Recent research showed that oral microbiomes (OMs), as the main source of lung microbiomes, were associated with lung cancer (LC), but the causal relationship and mechanisms remain unclear. This study aimed to explore the immune mechanisms of LC through the "OM - inflammatory proteins - LC" axis. Instrumental variables covering 43 oral microbial taxa, 91 circulating inflammatory proteins, and LC subtypes were obtained from large-scale genome-wide association study summary data of European origin. We employed Mendelian randomization (MR) analysis to validate causal links between the OM and LC and to assess the mediation effects of inflammatory proteins. The primary statistical method was the inverse variance weighted method, supplemented by leave-one-out analysis, MR-Egger regression, and Cochran's Q test to assess heterogeneity and pleiotropy. Finally, we calculated the effect size of inflammatory proteins as mediators. The results suggested that 9 oral microbial taxa and 20 inflammatory proteins were significantly associated with LC and its subtypes. Key findings included: Genus Rothia increased the risk of squamous cell carcinoma. At the species level, Haemophilus parainfluenzae protected against lung adenocarcinoma, whereas Megasphaera micronuciformis prevented small cell LC. Among the inflammatory proteins, the protein S100-A12 elevated adenocarcinoma risk, and STAM binding protein increased the risk of squamous cell carcinoma. Protective proteins included artemin (squamous cell carcinoma), cystatin D (adenocarcinoma), and interleukin 18 (both subtypes mentioned above). M. micronuciformis and overall LC had a causal relationship in which cystatin D played a mediating role. This study reveals a potential causal link between the OM, circulating inflammatory proteins, and LC. The protective effect of M. micronuciformis was mediated by cystatin D, highlighting a novel immune pathway. These findings provide biomarkers for early detection of LC and therapeutic targets for LC intervention.},
}

Humans
*Lung Neoplasms/microbiology/genetics
Mendelian Randomization Analysis
*Microbiota
Genome-Wide Association Study
*Mouth/microbiology
Inflammation

@article {pmid42888607,
year = {2026},
author = {Li, YD and Meng, H and Qu, R and Yang, SR and Wang, H},
title = {Gut microbiota, sleep and coronary artery disease: A Mendelian randomization study.},
journal = {Medicine},
volume = {105},
number = {42},
pages = {e49302},
doi = {10.1097/MD.0000000000049302},
pmid = {42888607},
issn = {1536-5964},
mesh = {Mendelian Randomization Analysis ; *Coronary Artery Disease/microbiology/genetics ; Humans ; *Gastrointestinal Microbiome/genetics/physiology ; Sleep Duration ; *Sleep/physiology ; Sleep Initiation and Maintenance Disorders/complications ; Risk Factors ; Chronotype ; },
abstract = {Inadequate and poor-quality sleep is increasingly recognized as a risk factor for coronary artery disease (CAD). Gut microbiota may play a role in sleep regulation. However, the associations between gut microbiota, sleep, and CAD risk, and the causal nature of these associations, remain unclear. We performed a 2-step Mendelian randomization analysis using summary-level data to assess the association between gut microbiota and CAD and the potential mediating roles of sleep-related traits (i.e., chronotype, insomnia, sleep duration, short sleep, and long sleep) herein. The inverse-variance weighted method served as the primary analysis, with several other complementary methods as sensitivity analyses. Our findings revealed that 2 gut microbial taxa were negatively associated with genetically predicted CAD risk, while 4 taxa, including species Veillonella unclassified (odds ratio: 1.054, 95% confidence interval: 1.010-1.101), showed positive associations. Regarding sleep-related traits, we found that insomnia (odds ratio: 1.553, 95% confidence interval: 1.081-2.230) and short sleep duration causally increased CAD risk, whereas longer sleep duration causally reduced CAD risk. The mediation Mendelian randomization analysis demonstrated that insomnia partially mediated the causal, predisposing effect of species Veillonella unclassified on increased CAD risk, with a proportion mediated of 5.7%. This study provides evidence for a causal relationship between specific gut microbial taxa and CAD risk, as well as the mediating role of insomnia in this relationship. These findings offer novel insights into potential strategies for CAD prevention through modulation of the gut microbiome and improvement of sleep quality.},
}

Mendelian Randomization Analysis
*Coronary Artery Disease/microbiology/genetics
Humans
*Gastrointestinal Microbiome/genetics/physiology
Sleep Duration
*Sleep/physiology
Sleep Initiation and Maintenance Disorders/complications
Risk Factors
Chronotype

@article {pmid42888864,
year = {2026},
author = {Schlager, JG and Stiefel, D and Patzer, K and Schloter, M and Foesel, BU and Zelzer, NM and French, LE and Gschwendtner, S and Hartmann, D},
title = {Basal Cell Carcinoma May Be Associated With Staphylococcus Dysbiosis.},
journal = {Experimental dermatology},
volume = {35},
number = {10},
pages = {e70371},
doi = {10.1111/exd.70371},
pmid = {42888864},
issn = {1600-0625},
support = {//Verein zur Förderung von Wissenschaft und Forschung an der Medizinischen Fakultät der LMU München e.V. (WiFoMed)/ ; },
mesh = {Humans ; *Dysbiosis/microbiology/complications ; *Basal Cell Carcinoma/microbiology ; *Skin Neoplasms/microbiology ; Skin Microbiome ; *Staphylococcus/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; Aged ; Male ; Middle Aged ; Skin/microbiology ; Aged, 80 and over ; Microbiota ; },
abstract = {There is growing evidence that a dysbiosis of the skin microbiome has an impact on carcinogenesis in cutaneous squamous cell carcinoma. However, the role of the microbiome in basal cell carcinoma (BCC) remains unclear due to limited, inconsistent, ex vivo studies. Here, we analysed the skin microbiome of patients with BCC, including the tumour lesion as well as perilesional skin from the same subject. Skin swabs from BCC and perilesional skin were taken prior to tumour surgery. After DNA extraction, we used a metabarcoding approach based on 16S rRNA gene amplicon sequencing to analyse the cutaneous bacterial communities. In total, 63 patients with BCC were included for analysis. Most tumour lesions were located on sun-exposed, sebaceous areas such as the nose, cheeks, and forehead. The genera Corynebacterium, Cutibacterium, and Staphylococcus predominated both in BCC and perilesional skin. However, the microbiome of BCC was reduced in overall bacterial richness, with a significant overabundance of amplicon sequence variants (ASV) assigned to the genus Staphylococcus, resulting in a reduced complexity in microbial networks. The dominating ASV assigned to Staphylococcus was also detected in perilesional skin regions, indicating that the microbial dysbiosis in BCC affected regions is caused by natural members of the healthy skin microbiome. The BCC microbiome is characterised by microbial dysbiosis, reflected by a reduced overall bacterial richness, fewer microbe-microbe interactions and a significant over-representation of Staphylococcus species compared with perilesional skin. Further long-read metagenomics and cultivation-based studies are needed to identify Staphylococcus species driving dysbiosis.},
}

Humans
*Dysbiosis/microbiology/complications
*Basal Cell Carcinoma/microbiology
*Skin Neoplasms/microbiology
Skin Microbiome
*Staphylococcus/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
Aged
Male
Middle Aged
Skin/microbiology
Aged, 80 and over
Microbiota

@article {pmid42888868,
year = {2026},
author = {Xie, S and Yang, Y and Tang, S and Zhou, L and Wang, J and Chan, JWY and Or, B and Li, N and Gong, S and He, Z and Ni, J and Liu, Y and Zhang, J and Chan, PKS and Chen, Z and Wong, SH and Mok, VCT and Chan, NY and Chau, SWH and Wing, YK and Huang, B},
title = {Habitual Diet, Gut Microbiome Dysbiosis, and α-Synucleinopathy Conversion in Isolated Rapid Eye Movement (REM) Sleep Behavior Disorder.},
journal = {Movement disorders : official journal of the Movement Disorder Society},
volume = {},
number = {},
pages = {},
doi = {10.1002/mds.70562},
pmid = {42888868},
issn = {1531-8257},
support = {05162876//Health and Medical Research Fund/ ; 06170676//Health and Medical Research Fund/ ; C4044-21G//Research Grants Council of Hong Kong/ ; //Center for Gut Microbiota Research, Faculty of Medicine, The Chinese University of Hong Kong/ ; },
abstract = {BACKGROUND: Accumulating evidence indicates that habitual diet, including plant-based dietary patterns, is associated with neurodegenerative α-synucleinopathy risk. However, the role of diet and its correlation with the gut microbiome in prodromal α-synucleinopathy, specifically among patients with isolated rapid eye movement (REM) sleep behavior disorder (iRBD), remains unclear.

OBJECTIVE: To evaluate dietary patterns, their interplay with gut microbial dysbiosis, and longitudinal effects on neurodegenerative progression in iRBD patients.

METHODS: We recruited 287 iRBD patients and 208 age- and sex-matched controls. Plant-based diet indices (PDIs) were derived from food frequency questionnaires. Shotgun metagenomic sequencing was performed in 456 subjects for diet-microbiome analyses. After a median follow-up of 4.2 years, 45 (15.7%) iRBD patients converted to α-synucleinopathies. Cox proportional hazards models assessed the associations between diet and neurodegenerative outcomes.

RESULTS: We found that iRBD patients exhibited lower healthful PDIs (adjusted odds ratio [aOR] 95% confidence interval [95% CI]: 0.48 [0.29-0.80], P = 0.005) but higher consumption of unhealthful plant-based foods (refined grains, sweets, and sweeteners). Diet-microbiome interaction analysis identified dietary associations for 84.3% of iRBD-related gut microbes, including co-occurrence between healthful PDI and Clostridium sp. AF20-17LB. Longitudinally, four dietary factors and five iRBD-related microbes were associated with neurodegenerative outcomes; specifically, higher coffee consumption was linked to a lower risk of progression to α-synucleinopathy (aHR [95% CI]: 0.30 [0.11-0.78], P = 0.01). Furthermore, mediation analyses indicated that the iRBD-enriched species Ruthenibacterium lactatiformans mediated the association between unhealthful PDI and dementia-first conversion.

CONCLUSIONS: Habitual diet in iRBD is associated with gut microbiome dysbiosis and predicts neurodegenerative progression. These findings highlight diet-microbiome interactions as modifiable targets for intervention in prodromal α-synucleinopathy. © 2026 The Author(s). Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.},
}

@article {pmid42888911,
year = {2026},
author = {Ezzafzafi, S and Bot, KKIM and Bernts, LHP and van Hest, RM and O'Brien, A and van Agtmael, MA and van Hattem, JM and Lantinga, MA},
title = {Antibiotic Stewardship in Cirrhosis: Current Recommendations and Clinical Challenges.},
journal = {United European gastroenterology journal},
volume = {14},
number = {8},
pages = {e70317},
doi = {10.1002/ueg2.70317},
pmid = {42888911},
issn = {2050-6414},
mesh = {Humans ; *Liver Cirrhosis/complications ; *Anti-Bacterial Agents/therapeutic use ; *Antimicrobial Stewardship/standards/methods ; *Antibiotic Prophylaxis/methods/standards ; *Peritonitis/microbiology/drug therapy/prevention & control/etiology ; *Bacterial Infections/prevention & control/drug therapy/microbiology ; Gastrointestinal Hemorrhage/etiology/drug therapy/prevention & control ; Practice Guidelines as Topic ; Esophageal and Gastric Varices/etiology ; Rifaximin/therapeutic use ; },
abstract = {Bacterial infections are a major cause of mortality in cirrhosis, with antibiotic prophylaxis and empirical treatment embedded in international guidelines. However, the prevalence of multidrug-resistant organisms and the epidemiology of infections have shifted considerably in recent decades. This review critically appraises the evidence underlying guideline recommendations on antibiotic prophylaxis for spontaneous bacterial peritonitis and acute variceal bleeding in cirrhosis, and antimicrobial management in acute liver failure. The evidence-underlying current recommendations is limited and predates the current era of widespread antimicrobial resistance, challenging their applicability in current practice. Emerging evidence suggests that primary prophylaxis should be reconsidered, alternatives such as rifaximin warrant further evaluation against established fluoroquinolone regimens, and shorter antibiotic courses may be non-inferior to standard durations. New double-blind placebo-controlled, non-inferiority and Bayesian trials are needed to evaluate antibiotic regimens and microbiome- and barrier-directed interventions, supported by improved diagnostics, while minimising treatment duration, toxicity and selection for antimicrobial resistance.},
}

Humans
*Liver Cirrhosis/complications
*Anti-Bacterial Agents/therapeutic use
*Antimicrobial Stewardship/standards/methods
*Antibiotic Prophylaxis/methods/standards
*Peritonitis/microbiology/drug therapy/prevention & control/etiology
*Bacterial Infections/prevention & control/drug therapy/microbiology
Gastrointestinal Hemorrhage/etiology/drug therapy/prevention & control
Practice Guidelines as Topic
Esophageal and Gastric Varices/etiology
Rifaximin/therapeutic use

@article {pmid42888923,
year = {2026},
author = {Hafiane, A and Kiss, RS and Favari, E and Amedei, A and Parolini, C},
title = {The Hidden Conductor: HDL-Gut Microbiome Interplay in the Pathophysiology of Inflammatory-Based Diseases.},
journal = {BioFactors (Oxford, England)},
volume = {52},
number = {5},
pages = {e70162},
doi = {10.1002/biof.70162},
pmid = {42888923},
issn = {1872-8081},
support = {//Dipartimenti di Eccellenza/ ; },
mesh = {Humans ; *Cardiovascular Diseases/microbiology/metabolism/pathology/genetics/physiopathology ; *Inflammatory Bowel Diseases/microbiology/metabolism/pathology/genetics/physiopathology ; *Gastrointestinal Microbiome ; Animals ; *Neurodegenerative Diseases/microbiology/metabolism/pathology/genetics/physiopathology ; *Lipoproteins, HDL/metabolism/genetics ; *Neoplasms/microbiology/metabolism/pathology/genetics ; *Inflammation/microbiology/metabolism ; },
abstract = {High-density lipoprotein (HDL) is a cholesterol transporter that plays a well-defined role in reverse cholesterol transport. In addition, HDL shows anti-inflammatory and immunomodulatory functions mainly due to its ability to decrease the cholesterol content in lipid rafts, thus strongly influencing the membrane fluidity and the right localization/functionality of membrane-associated proteins (i.e., receptors/ligands) and their signal transduction pathways. Diverse experimental and clinical studies support the existence of a dynamic and complex relationship between HDL functionality and the gut microbiome (GM), with relevant implications for the pathophysiology of many widespread inflammatory-based diseases, such as cardiovascular disease (CVD), inflammatory bowel disease (IBD), neurodegenerative disorders (NDDs) and cancer. Host factors (age, genes, dietary and lifestyle habits, medications) or environmental conditions may strongly negatively affect both the HDL system and the GM composition and function, promoting chronic low-grade inflammatory conditions that may exacerbate susceptibility to these human pathologies. Therefore, it can be hypothesized that the HDL-GM relationship may represent a novel therapeutic target to decrease the burden of these inflammatory-based pathologies. This review summarizes current data about the role of HDL and GM in the pathogenesis of CVD, IBD, NDDs and cancer, as well as findings that support the HDL-GM interplay as a crucial factor in the development of these relevant illnesses. Finally, we discuss the shortcomings of this relationship delineating the future directions to address them.},
}

Humans
*Cardiovascular Diseases/microbiology/metabolism/pathology/genetics/physiopathology
*Inflammatory Bowel Diseases/microbiology/metabolism/pathology/genetics/physiopathology
*Gastrointestinal Microbiome
Animals
*Neurodegenerative Diseases/microbiology/metabolism/pathology/genetics/physiopathology
*Lipoproteins, HDL/metabolism/genetics
*Neoplasms/microbiology/metabolism/pathology/genetics
*Inflammation/microbiology/metabolism

@article {pmid42889004,
year = {2026},
author = {Bao, Z},
title = {Editorial: The gut-liver axis in MASLD: microbiome, metabolism, disease progression and therapeutic pathways.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1947178},
doi = {10.3389/fmed.2026.1947178},
pmid = {42889004},
issn = {2296-858X},
}

@article {pmid42889019,
year = {2026},
author = {Wahid, Z and Ahmad, AMR and Zulfiqar, F and Shah, SHBU and Mohammadi, N},
title = {Postbiotics Unveiled: The Next Emerging Trend in Functional Foods.},
journal = {Food science & nutrition},
volume = {14},
number = {10},
pages = {e72485},
doi = {10.1002/fsn3.72485},
pmid = {42889019},
issn = {2048-7177},
abstract = {The global population is expected to reach 9.7 billion by 2050, with demand for food increasing by up to 56%. Postbiotics are a safe and reliable substitute for probiotics, which are described as preparations of non-viable bacteria and/or their metabolic byproducts. Data for this narrative review was collected using Goggle scholar and PubMed from 2006 to 2026. Major bioactive compounds such as short-chain fatty acids, peptides, polysaccharides, vitamins, and cell fragments contribute to immunomodulatory, antioxidant, metabolic, and gut-brain axis effects. Preclinical and clinical research shows that they can improve insulin sensitivity, control cytokine signaling, strengthen epithelial barrier integrity, and protect against obesity, type 2 diabetes mellitus, and depression. Postbiotics have also been found to improve mineral absorption and folate synthesis, and possess anti-sarcopenic actions. Several commercial products are available because of their health benefits. Thus, postbiotics are a revolutionary development in microbiome-based treatments; however, to completely understand their therapeutic potential, it is necessary to standardize, achieve mechanistic clarity, and ensure regulatory alignment.},
}

@article {pmid42889038,
year = {2026},
author = {Zhu, C and Wang, X and Feng, L and Xu, M and Huang, Z and Chen, W and Liu, L},
title = {IMicAP: an intelligent microbial application platform for knowledge-driven microbiome research.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1955928},
doi = {10.3389/fmicb.2026.1955928},
pmid = {42889038},
issn = {1664-302X},
abstract = {BACKGROUND: Microorganisms play a pivotal role in health and disease, yet microbial research is hindered by fragmented data, heterogeneous knowledge representation, and a lack of integrated analytical tools. Existing databases and knowledge graphs often focus narrowly on genomic information, leaving critical metabolomic and literature-based associations underdeveloped.

RESULTS: We developed the Intelligent Microbial Application Platform (IMicAP), an AI-driven, open-access web platform that integrates 12 microbial databases and over 35 million articles. IMicAP delivers 5 core modules: (1) Knowledge Query module for rapid data retrieval; (2) Knowledge Graph module for multi-hop reasoning and hypothesis generation; (3) Intelligent Question-Answering module for professional natural language dialogue in the field of microbiology; (4) Genome Browser module for genomic visualization; and (5) 16S rRNA Sequencing Analysis module for zero-code microbial bioinformatics analysis. Using curated microbe-disease and microbe-small molecule relations extracted with biomedical language models, IMicAP enables context-aware exploration of microbial relations.

CONCLUSION: IMicAP (available at: https://www.imicap.com:8443) is the first comprehensive, open-access, AI-powered microbial platform designed to bridge the gap between fragmented microbial data and actionable biological insights. It directly addresses 4 key limitations in existing resources: (1) Fragmented analysis without integrated workflows; (2) Narrow disease scope covering only one or two disease types; (3) Incomplete knowledge from restricted data sources; and (4) neglect of metabolomic information. IMicAP serves as a versatile resource for advancing microbiome research and translational discoveries. Future development focus on expanding microbial coverage, enhancing reasoning scalability, and evolving toward a dual knowledge-and-data-driven architecture to further support mechanistic discovery in microbial systems biology.},
}

@article {pmid42889045,
year = {2026},
author = {Park, SH and Cheon, DS and Cho, TJ and Kim, SA},
title = {Pathogen detection and microbial community characterization in clinically symptomatic pigs from commercial farms.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1947134},
doi = {10.3389/fvets.2026.1947134},
pmid = {42889045},
issn = {2297-1769},
abstract = {Effective swine disease control requires continuous monitoring of major pathogens and a comprehensive understanding of microbial community dynamics under disease conditions. Here, we collected lung, oral fluid, and fecal samples from clinically symptomatic pigs on commercial farms in South Korea. Molecular diagnostics targeting major respiratory and enteric pathogens were performed to assess infection status, alongside 16S rRNA gene sequencing to simultaneously characterize respiratory and enteric microbiota. Most respiratory pathogens were detected at higher rates in oral fluid than in lung samples. Pasteurella multocida was the most frequently detected pathogen overall, while porcine reproductive and respiratory syndrome virus (PRRSV) showed the highest detection rate in lung samples. Among enteric pathogens, rotavirus showed the highest detection rate. Microbiome profiling revealed that lung samples had the lowest species diversity, while distinct microbial community structures were observed among lung, oral fluid, and fecal samples. Prevotellaceae-associated genera were dominant in fecal samples. The lung microbiota was characterized by dominance of a limited number of taxa, including Escherichia-Shigella and Actinobacillus, whereas oral fluid exhibited a more evenly distributed microbial composition enriched in Moraxella and Streptococcus. Differentially abundant taxa and contrasting predicted functional profiles were identified between Clostridium perfringens-positive and -negative groups, indicating a potential association between Clostridium perfringens presence and gut microbial community composition. This study integrates molecular diagnostics with microbiome profiling in clinically diseased pigs under field conditions. These findings provide field-based evidence to support microbiome-informed monitoring and interpretation of pathogen-associated changes in swine production systems.},
}

@article {pmid42889144,
year = {2026},
author = {Powell, AM and Sobel, JD and Muzny, CA},
title = {Management of Recurrent Vaginitis.},
journal = {Current obstetrics and gynecology reports},
volume = {15},
number = {1},
pages = {41},
doi = {10.1007/s13669-026-00494-w},
pmid = {42889144},
issn = {2161-3303},
abstract = {PURPOSE OF REVIEW: This review summarizes current evidence regarding the pathogenesis, diagnosis, and management of recurrent BV, recurrent VVC, and persistent trichomoniasis while highlighting emerging therapies and research priorities.

RECENT FINDINGS: Recurrent BV is driven by persistence of a polymicrobial biofilm on vaginal epithelial cells, failure to restore a Lactobacillus-dominant vaginal microbiome following antibiotic therapy, and reinfection from untreated sexual partners. Emerging therapeutic approaches including live biotherapeutic products, vaginal microbiota transplantation, and male partner treatment seek to address these mechanisms beyond conventional antibiotic suppression. In contrast, recurrent vulvovaginal candidiasis primarily reflects host susceptibility and immune dysregulation rather than persistent infection, making long-term suppressive antifungal therapy the cornerstone of management while newer antifungal agents expand treatment options for selected patients. Persistent trichomoniasis most commonly results from reinfection or incomplete therapy, although antimicrobial resistance remains an important consideration requiring specialized diagnostic testing and alternative treatment regimens.

SUMMARY: Recurrent vaginitis is a common and frustrating clinical problem that substantially impairs women's quality of life and accounts for frequent healthcare utilization. Although bacterial vaginosis (BV), vulvovaginal candidiasis (VVC), and trichomoniasis (TV) share overlapping signs and symptoms, the mechanisms underlying recurrence differ considerably and require disease-specific management strategies.},
}

@article {pmid42889178,
year = {2026},
author = {Liu, Q and Xie, H and Lin, F and Huang, W and Lao, J},
title = {Probiotics and synbiotics as adjunctive therapies for heart failure: a systematic review with network and pairwise meta-analyses.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1898538},
doi = {10.3389/fnut.2026.1898538},
pmid = {42889178},
issn = {2296-861X},
abstract = {OBJECTIVE: This study aimed to evaluate the use of probiotics and synbiotics as microbiome-directed adjunctive therapies for heart failure (HF), while explicitly determining whether any eligible prebiotic-only trials existed.

METHODS: We searched eight English- and Chinese-language databases from inception to 1 May 2026 and conducted expanded sensitivity searches in PubMed, Embase, and Web of Science on 15 July 2026. Random-effects network meta-analysis (NMA) was used only for connected multi-node evidence; two-node evidence was analyzed pairwise. As placebo, usual care, and food comparators were not clinically exchangeable, comparator-stratified sensitivity analyses of direct evidence were conducted using restricted maximum likelihood (REML) and Hartung-Knapp (HK) confidence intervals (CIs).

RESULTS: A total of 12 randomized studies were included in the systematic review (14 reports); 11 contributed to at least one primary or sensitivity quantitative analysis, and 10 contributed to the primary analyses. The revision-stage search audit identified no additional eligible randomized trials and no eligible prebiotic-only trials. Across all the trial populations, 1,021 participants were randomized, 973 of whom were allocated to review-eligible arms. The left ventricular ejection fraction (LVEF) network included 7 studies and 539 participants in the analysis set; however, this network was star-shaped, had no closed loops, and depended on a combined comparator node. The exploratory NMA estimate for multi-strain bacterial probiotics versus the combined comparator was a mean difference (MD) of 2.13 percentage points (95% confidence interval [CI] -0.10 to 4.35). The comparator-stratified sensitivity analysis for usual care yielded an MD of 1.83 percentage points (95% CI -2.33 to 5.98). All synthesized results were assessed as having either some concern or a high risk of bias. The effect estimates were generally imprecise, and the certainty of evidence was low or very low. Adverse event definitions and denominators were inconsistent.

CONCLUSION: The available evidence is sparse and affected by significant non-transitivity, risk of bias, and imprecision. Network comparisons and rankings should be considered hypothesis-generating; therefore, no probiotic or synbiotic adjunct can be recommended for routine HF management.

CRD420261413595. Public URL: https://www.crd.york.ac.uk/PROSPERO/view/CRD420261413595.},
}

@article {pmid42889247,
year = {2026},
author = {Fu, S and Zhou, F and Gong, L and Ye, A},
title = {Amelioration of chronic inflammation, insulin resistance, and gut microbiota homeostasis by a combination of Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus in obese type 2 diabetic mice.},
journal = {Nutrition research and practice},
volume = {20},
number = {5},
pages = {800-819},
doi = {10.4162/nrp.2026.20.5.800},
pmid = {42889247},
issn = {1976-1457},
abstract = {BACKGROUND/OBJECTIVES: To examine the effects of a combination of live Bifidobacterium, Lactobacillus, Enterococcus, and Bacillus (CBLEB) on glucose/lipid metabolism, inflammation, gut microbiota, and related mechanisms in obese type 2 diabetes mellitus (T2DM) mice.

MATERIALS/METHODS: Obese T2DM mice were established by feeding mice a high-fat diet for four weeks, followed by a single intraperitoneal injection of streptozotocin (100 mg/kg). The mice were then divided randomly into 5 groups (n = 8/group): normal control (NC), T2DM model, CBLEB (585 mg/kg/d, by gavage), dimethylbiguanide (DMBG, 200 mg/kg/d, by gavage), and CBLEB+DMBG combination. All treatments were administered daily for four weeks. The body weight and fasting blood glucose were monitored weekly. An oral glucose tolerance test was performed to assess the glucose tolerance. The serum levels of lipids (triglycerides, total cholesterol, high-density lipoprotein cholesterol, and low-density lipoprotein cholesterol), insulin, and inflammatory factors (tumor necrosis factor [TNF]-α, interleukin [IL]-1β, IL-6, IL-10, and lipopolysaccharide) were measured by enzyme-linked immunosorbent assay. Pancreatic IL-6 and TNF-α expression was detected by immunohistochemistry. The histopathological changes in the pancreas, colon, and adipose tissues were evaluated by hematoxylin and eosin staining. The protein expression of insulin receptor substrate 1 (IRS-1)/p-IRS-1 (Ser307), Toll-like receptor 4 (TLR4)/MyD88, tight junction proteins (zonula occludens protein 1 [ZO-1]/claudin 1 [CLDN1]/occludin), and B-cell lymphoma/leukemia-2 (Bcl-2)-associated X protein A (BAX)/Bcl-2 was analyzed by Western blot. The gut microbiota composition was profiled by 16S rRNA gene sequencing.

RESULTS: CBLEB significantly improved the weight gain, hyperglycemia, insulin resistance (IR), dyslipidemia, reduced adipocyte size, suppressed systemic inflammation, and alleviated pancreatic and colonic damage in T2DM mice. The combination of CBLEB and DMBG showed the most pronounced improvements in metabolic and inflammatory parameters. Western blot showed that CBLEB inhibited TLR4/MyD88 signaling, enhanced insulin signaling (IRS-1/p-IRS-1), repaired the intestinal barrier (ZO-1/CLDN1/occludin), and regulated the apoptotic balance (BAX/Bcl-2). Gut microbiota analysis suggested that CBLEB remodeled the gut microbiota, with a functional prediction suggesting shifts in the metabolic pathways and a decrease in the abundance of Escherichia spp.

CONCLUSION: CBLEB ameliorated systemic inflammation and IR in obese T2DM mice through gut microbiota modulation, intestinal barrier restoration, and suppression of inflammatory pathways.},
}

@article {pmid42889337,
year = {2026},
author = {Maghembe, RS and Damian, D and Bahati, S and Makaranga, A},
title = {Microbiome-Endocannabinoidome Crosstalk as an Immunometabolic Rheostat in Inflammatory Disease.},
journal = {FASEB bioAdvances},
volume = {8},
number = {10},
pages = {e70163},
doi = {10.1096/fba.2026-00201},
pmid = {42889337},
issn = {2573-9832},
abstract = {Chronic inflammatory diseases reflect disrupted coordination among microbial ecology, epithelial barriers, lipid signaling, and immunity. The microbiome-endocannabinoidome (eCBome) axis is already recognized as a regulator of metabolism, permeability, and inflammatory tone; the unresolved issue is how to distinguish direct crosstalk from parallel or associative changes. This review therefore operationalizes the axis as an immunometabolic rheostat defined by five measurable domains: microbial functions and metabolites, compartment-specific eCBome ligands and enzymes, barrier integrity and microbial translocation, immune-cell programming, and tissue or clinical outcomes. We distinguish classical endocannabinoids (anandamide and 2-arachidonoylglycerol) from the endocannabinoid-related N-acylethanolamines palmitoylethanolamide and oleoylethanolamide, which act prominently through PPARα, TRPV1, GPR119, and related pathways. Evidence is appraised as direct causal, mechanistically supportive, associative, or hypothesis-generating. The strongest causal foundation links microbiota manipulation to intestinal eCBome tone, permeability, and metabolic endotoxemia, while disease-specific evidence is most developed in obesity-associated inflammation and inflammatory bowel disease. Engineered Lactobacillus paracasei platforms that produce PEA or OEA in situ provide particularly informative proof-of-concept because they couple a defined microbial perturbation to lipid-mediator release, receptor-dependent barrier effects, and inflammatory or metabolic outcomes. By contrast, evidence in MASLD/MASH, neuroinflammation, and systemic autoimmunity remains more compartment-dependent and heterogeneous. Clinical translation must account for the psychiatric toxicity that ended centrally active CB1 antagonism with rimonabant, the target and off-target complexity of FAAH/MAGL inhibition, and limitations of surrogate barrier biomarkers. A causal roadmap should combine gnotobiotic and loss-of-function models, isotope tracing, organoids, and gut-on-chip systems with tissue-resolved lipidomics and longitudinal, biomarker-enriched human trials.},
}

@article {pmid42889412,
year = {2026},
author = {Nazir, A and Nazir, R and Sharma, S and Amna, T and Ahmed, ZFR},
title = {Epigenetic regulation of immune checkpoint signaling by microbial metabolites: mechanisms, therapeutic potential, and future perspectives.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1970192},
doi = {10.3389/fimmu.2026.1970192},
pmid = {42889412},
issn = {1664-3224},
mesh = {Humans ; *Epigenesis, Genetic/immunology ; *Signal Transduction/immunology ; Animals ; *Immune Checkpoint Proteins/metabolism/genetics/immunology ; *Gastrointestinal Microbiome/immunology ; Neoplasms/immunology/therapy ; },
abstract = {The gut microbiome has emerged as an important regulator of host immunity through the production of diverse bioactive metabolites. The gut microbiome has emerged as an important regulator of host immunity through the production of diverse bioactive metabolites. Microbiota-derived metabolites influence immune cell function and contribute to the maintenance of immune homeostasis, serving as key molecular mediators of host-microbiota communication. Importantly, while evidence is emerging that these metabolites affect immune checkpoint signaling, less is known about the molecular mechanisms behind these interactions. Recent research demonstrated that SCFAs, secondary bile acids, indoles derived from tryptophan, inosine, polyamines and other microbial metabolites affect the immune checkpoints through epigenetics, metabolism, receptor signaling, and intracellular pathway modulation. These interactions affect the expression and functioning of key immune checkpoint molecules such as PD-1, PD-L1, CTLA-4, LAG-3, TIGIT, TIM-3 and VISTA. In this review, we summarize current knowledge regarding the Metabolite-Immune Checkpoint Axis, stressing the role of metabolites derived from microbiota in the regulation of immune checkpoints. We elaborate on the molecular mechanisms of these interactions and their significance in the context of cancer, autoimmune disorders, chronic inflammatory disorders, and infectious diseases. We also provide insights regarding the developing therapeutic strategies based on microbiome-modulated therapy. Finally, we highlight key knowledge gaps and future research directions required for the clinical translation of microbiome-based personalized therapies.},
}

Humans
*Epigenesis, Genetic/immunology
*Signal Transduction/immunology
Animals
*Immune Checkpoint Proteins/metabolism/genetics/immunology
*Gastrointestinal Microbiome/immunology
Neoplasms/immunology/therapy

@article {pmid42889547,
year = {2026},
author = {Sampson, V},
title = {The forgotten organ: Why the oral microbiome belongs in every physician's toolkit.},
journal = {Future healthcare journal},
volume = {13},
number = {3},
pages = {100560},
doi = {10.1016/j.fhj.2026.100560},
pmid = {42889547},
issn = {2514-6645},
abstract = {The oral cavity is the most densely colonised microbial niche in the human body after the gut - over 700 species and an estimated two billion bacteria (Deo and Deshmukh, 2019) - yet it remains conspicuously absent from the systemic health conversation. Mounting evidence links oral microbial dysbiosis to more than 50 systemic conditions (Peng et al, 2022), including cardiovascular disease, type 2 diabetes (Preshaw et al, 2026), adverse pregnancy outcomes, rheumatoid arthritis and Alzheimer's. Despite this, dentistry and medicine continue to operate as parallel systems, with oral health excluded from most general health screens, NHS commissioning structures and undergraduate medical curricula. This narrative review analyses current evidence on the oral microbiome and oral-systemic disease, outlines three biological mechanisms by which the oral cavity drives systemic disease, and sets out five practical, author-proposed steps physicians can take to integrate oral health into routine practice. The case for action is no longer scientific - it is structural.},
}

@article {pmid42889669,
year = {2026},
author = {Sun, G and Yang, J and Lv, S and Yu, L and Si, L},
title = {The microbiome-metabolite-vaccine axis: context-dependent modulators of immunogenicity and durability.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1972642},
doi = {10.3389/fimmu.2026.1972642},
pmid = {42889669},
issn = {1664-3224},
mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/immunology ; *Immunogenicity, Vaccine ; *Vaccines/immunology ; Probiotics ; Vaccination ; },
abstract = {Vaccine responses vary markedly between individuals, yet age, genetics, prior antigen exposure, comorbidity, nutrition and vaccine platform explain only part of this heterogeneity. The intestinal microbiome is a candidate modulator through microbial metabolites and parallel non-metabolic signals. Human studies link microbial features to vaccine outcomes, but taxa rarely replicate across geography, age and platform. Small randomised antibiotic studies identify effects of treatment assignment, not necessarily microbiome mediation; infant microbial rescue has been demonstrated in mice rather than infants. Amongst the pathways considered, short-chain fatty acids have the largest mechanistic evidence base, predominantly preclinical, but acetate, propionate and butyrate differ in targets, exposure and direction of effect, and direct human vaccine mediation remains unestablished. Null findings for BNT162b2 in microbiota-depleted mice and for overall antibody responses in an older-adult probiotic trial argue against universal microbiome dependence or probiotic benefit. We organise the evidence around a microbial function-mediator-exposure-immune-checkpoint-endpoint chain, retaining a primary focus on metabolites. Vaccine take, peak antibody, decay and recall are distinguished from clinical protection. We also separate microbiome-modifying probiotics from antigen-delivery platforms. A decision-gated workflow links signature discovery, source and target verification, independent validation, randomised intervention and demonstrated clinical utility. Microbiome-guided vaccination remains a research strategy rather than an established clinical practice.},
}

Humans
Animals
*Gastrointestinal Microbiome/immunology
*Immunogenicity, Vaccine
*Vaccines/immunology
Probiotics
Vaccination

@article {pmid42889749,
year = {2026},
author = {Zhang, Z and Zhang, Y and Zhao, K and Cheng, G and Lu, Z and Wang, D and Liu, Y and Wu, J and Wang, L and Zhang, L and Ye, X and Yu, L and Zhang, W and Li, Y},
title = {Domesticated bacterial origin genes regulate homeostasis of the insect gut microbiome and empower adaptation.},
journal = {iMeta},
volume = {},
number = {},
pages = {e70179},
doi = {10.1002/imt2.70179},
pmid = {42889749},
issn = {2770-596X},
abstract = {Sap-sucking insects, represented by the globally distributed leafhoppers, have evolved a wide range of adaptive traits and play multiple ecological roles. However, their successful survival strategies in nature remain poorly understood. To explore the adaptive mechanisms of sap-sucking insects, we established a research system using three representative leafhopper species from the same family and found that they have acquired multiple cholesterol-dependent cytolysins (CDCs) derived from gram-positive bacterial genes. Furthermore, we demonstrated that these CDCs have been domesticated and co-evolved with leafhoppers, ultimately participating in various life activities of the host. Specifically, some CDCs exhibit high cytotoxicity, are specifically expressed in the egg serosa, and affect the feeding behaviors of leafhopper predators; others show non-cytotoxic activity, are specifically expressed in the gut, and may regulate leafhopper growth and development by potentially maintaining the homeostasis of the leafhopper gut microbiome. This study uncovers leafhoppers as a paradigm for understanding how organisms can borrow microbial innovations to address ecological challenges and thrive as agricultural pests. It provides a comprehensive perspective to bridge the genotypes of acquired genes with the phenotypes of adaptive traits and demonstrates how homologous genes from donor organisms undergo functional differentiation in recipient hosts, enabling them to exploit new ecological niches. By decoding these mechanisms, we not only gain fundamental insights into evolutionary processes but also develop powerful strategies for sustainable pest management.},
}

@article {pmid42889776,
year = {2026},
author = {Gupta, N and Rengasamy, M and Kumar, RK and Sethuraman, G and Kumar, KP and Sanklecha, M and Verma, R and Mittal, M and Joshi, V and Natarajan, S and Kerketta, JA and Pal, T and Vasani, R and Ramamoorthy, R and Menon, S and Thakor, P and Naik, I and Chamle, V and Bangale, N and Gvalani, A},
title = {Prevention and Management of Pediatric Sensitive Skin Conditions in India: A Modified Delphi Consensus.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e116261},
doi = {10.7759/cureus.116261},
pmid = {42889776},
issn = {2168-8184},
abstract = {Sensitive skin poses significant dermatological challenges in the pediatric population, necessitating thorough exploration and understanding. In this study, we aim to provide neonatologists, pediatricians, dermatologists, and allergists in India with consensus-based recommendations for the prevention and management of sensitive skin in the pediatric age group. A modified Delphi method was used to arrive at a consensus. A group of 15 experts with experience in pediatric skincare constituted the panel. Panel members representing diverse specialties from the major regions of India participated in the consensus process. Statements were developed based on a structured review of the literature identified through PubMed/Medical Literature Analysis and Retrieval System Online (MEDLINE) (January 2000 to May 2024; updated in March 2025) using the keywords "sensitive skin," "pediatric," "emollient," "prevention," and other related terms. Ninety-six clinically relevant questions and/or statements were drafted for discussion: (i) burden, pathophysiology, and challenges in the diagnosis of sensitive skin; (ii) symptoms, risk factors, and consequences; (iii) clinical diagnosis; (iv) prevention and management; and (v) the positioning of colloidal oatmeal-based emollients in managing and preventing sensitive skin in the pediatric population. The consensus level was classified into agreement (mean score of ≥4), no consensus, and exclusion (mean score of <4 after the second round). The process involved two rounds of Delphi surveys and one round of discussion. The experts unanimously agreed that diaper dermatitis, xerosis, and atopic dermatitis (AD) were the most prevalent sensitive skin conditions in children. Physical examinations and assessments of clinical and medical histories were the most effective primary diagnostic methods for identifying sensitive skin. The experts recommended moisturizers/emollients as a cornerstone for managing sensitive skin conditions and enhancing skin health and quality of life (QoL). Emollients should hydrate the skin, repair the skin barrier, and restore ceramide and microbiome balance, all while avoiding irritants. The experts recommended colloidal oatmeal-based emollients in xerosis and AD and as supportive adjunctive care alongside allergen avoidance in allergic contact dermatitis because of their prebiotic properties, soothing effects, and ability to activate endogenous ceramide production, which helps restore the skin's barrier and integrity. In the panel's view, the early and long-term usage of colloidal oatmeal-based emollients helps in the reduction of flare severity and frequency and, potentially, reliance on corticosteroids.},
}

@article {pmid42889795,
year = {2026},
author = {Cheng, Z and Rong, P},
title = {Roles and mechanisms of halophilic/salt-tolerant microorganisms in mitigating plant salt stress and promoting growth.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1848153},
doi = {10.3389/fmicb.2026.1848153},
pmid = {42889795},
issn = {1664-302X},
abstract = {Soil salinization is a major constraint on global agricultural productivity and food security, largely because excess salts disrupt osmotic balance, nutrient acquisition, ion homeostasis, and redox stability in plants. Halophilic and salt-tolerant microorganisms, including plant growth-promoting rhizobacteria, endophytes, and fungi, have emerged as promising biological tools for improving crop performance in saline environments. This review synthesizes current evidence on how these microorganisms mitigate salt stress and promote plant growth across diverse crop systems. The major mechanisms include modulation of phytohormone homeostasis, especially through auxin production and ACC deaminase activity; enhanced nutrient acquisition via nitrogen fixation, phosphate solubilization, and siderophore production; maintenance of ionic balance through reduced Na+ toxicity and improved K+/Na+ homeostasis; reinforcement of antioxidant defense systems; stimulation of osmolyte accumulation; and effective rhizosphere colonization through exopolysaccharide secretion and biofilm formation. Representative studies in rice, wheat, maize, tomato, soybean, cucumber, chickpea, common bean, quinoa, and banana consistently show improvements in germination, biomass, physiological resilience, and, in some cases, yield under salinity stress. However, important challenges remain, including strain specificity, inconsistent field performance, limited mechanistic resolution, ecological safety concerns, and the difficulty of translating laboratory strains into stable commercial products. Future progress will depend on multi-omics-guided mechanism dissection, precision microbiome engineering, improved formulation and delivery systems, and rigorous long-term field validation. Overall, halophilic/salt-tolerant microorganisms represent a promising strategy for saline agriculture and sustainable crop production.},
}

@article {pmid42889944,
year = {2026},
author = {Xiang, ZY and Yang, XH and Lan, WY and Xiao, XY and Huang, Q and Yang, LL},
title = {Natural products targeting mitochondrial homeostasis: a four-dimensional framework integrating dynamics, mitophagy, pharmacokinetics, and translational safety.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1911495},
doi = {10.3389/fphar.2026.1911495},
pmid = {42889944},
issn = {1663-9812},
abstract = {BACKGROUND: Dysregulated mitochondrial dynamics, including fission, fusion, biogenesis, and mitophagy, underlie the pathogenesis of many diseases. Natural products have the potential for multi-target therapy, but insufficient understanding of their mechanisms of action and pharmacokinetic limitations hinder their clinical translation.

OBJECTIVE: This review proposes a regulatory framework covering the four dimensions of biogenesis, morphology, quality control, and defense, aiming to systematically clarify how natural products regulate mitochondrial function and critically evaluate their translational potential. The framework emphasizes that inter-organelle contact platforms, such as mitochondria-endoplasmic reticulum contact sites (MERCs) and mitochondrial-lysosomal contact sites (MLCs), are key sites through which natural products exert regulatory effects.

METHODS: Major scientific databases, including PubMed, Web of Science, and Scopus, were searched, and evidence on mechanisms, pharmacokinetics, and toxicology from preclinical and clinical studies was comprehensively reviewed.

RESULTS: Natural products can selectively regulate key mitochondrial pathways and regulatory nodes, including the AMPK/SIRT1/PGC-1α axis involved in mitochondrial biogenesis, the DRP1 axis involved in mitochondrial fission, and the PINK1/Parkin pathway involved in mitophagy. Representative metabolites include resveratrol, curcumin, and Coptis chinensis-derived alkaloids. A key finding of this review is that the intestinal microbiota plays an important role in converting low-bioavailability precursors, such as tannins, into systemically active metabolites, such as urolithin A (UA), thus inducing mitophagy. Although these metabolites usually show strong activity in vitro, their low oral bioavailability and rapid metabolism lead to significant pharmacokinetic/pharmacodynamic (PK/PD) mismatch, which remains a major obstacle to their clinical translation.

CONCLUSION: Natural products are powerful multidimensional regulators of mitochondrial homeostasis. In order to fully realize their therapeutic potential, strategies must be adopted to overcome PK/PD mismatch, including the development of targeted delivery systems, in-depth analysis of microbiome-metabolite interactions, and the integration of artificial intelligence and CRISPR-based technological innovation to support precision therapy.},
}

@article {pmid42890090,
year = {2026},
author = {Leng, M and Wei, Z},
title = {Pathological microbial niches in diabetic foot ulcers: a host-microbe framework for impaired repair and niche-based stratification.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1926191},
doi = {10.3389/fcimb.2026.1926191},
pmid = {42890090},
issn = {2235-2988},
mesh = {Humans ; *Diabetic Foot/microbiology/pathology ; Biofilms/growth & development ; *Host Microbial Interactions ; *Wound Healing ; Microbiota ; Host-Pathogen Interactions ; },
abstract = {Diabetic foot ulcers (DFUs) are commonly described through the clinical triad of hyperglycaemia, ischaemia and infection. That language is useful for bedside decision-making, but it does not fully explain why some wounds remain inflamed and open despite debridement, offloading, antimicrobial therapy, vascular assessment and modern wound care. Here we develop a conceptual review framework in which many non-healing DFUs are interpreted as pathological microbial niches: local tissue regions where microbial persistence and host repair failure reinforce each other. Hyperglycaemia, impaired perfusion, hypoxia, neuropathic pressure injury, necrotic material and extracellular matrix degradation generate ecological space for microbial survival. Microbial products, biofilm-like spatial organisation, strain-level traits, fungi and polymicrobial interactions then amplify neutrophil extracellular traps, inflammasome signalling, protease release, fibroblast dysfunction, endothelial impairment and defective re-epithelialisation. The result is not a linear sequence from colonisation to infection to inflammation, but a self-reinforcing loop in which microbial adaptation and host non-healing programs become difficult to separate. We summarise evidence from chronic wound microbiome studies, biofilm histology, strain-level and fungal analyses, host transcriptomics, single-cell data and emerging spatial omics, while emphasising the boundaries of each evidence type. The central question is not whether microbes can be detected in DFU tissue, but whether they are viable, metabolically active, spatially organised and positioned close enough to host cells to alter repair behaviour. We propose an operational definition of the pathological microbial niche and a translational scheme for biofilm-dominant, ischaemia-dominant, protease-dominant, senescence-dominant and immune-resolution-failure wound patterns. This framing may help move DFU microbiome research from descriptive association toward mechanism-based stratification and more rational combinations of source control, vascular optimisation, antimicrobial therapy and repair-directed treatment.},
}

Humans
*Diabetic Foot/microbiology/pathology
Biofilms/growth & development
*Host Microbial Interactions
*Wound Healing
Microbiota
Host-Pathogen Interactions

@article {pmid42890099,
year = {2026},
author = {Bertola, A and Wenner, N and Rocha, LL and Keys, TG and Diard, M},
title = {Microbiota-constrained bacterial density limits phage infection in the gut and allows persistence of susceptible cells.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117433},
doi = {10.1016/j.isci.2026.117433},
pmid = {42890099},
issn = {2589-0042},
abstract = {With the rise of antibiotic resistance, bacteriophage-based treatments against bacterial infections have regained momentum. However, phage therapy has so far shown only moderate success in complex environments like the mammalian gut, where phages are particularly promising tools for microbiome engineering and specific elimination of opportunistic pathogens. Here, we use different murine models of intestinal colonization to quantitatively assess the minimal population size of susceptible Escherichia coli cells that is required for phage replication in the gut (replication threshold). We found that the composition of the intestinal microbiota is a key factor shaping phage-bacteria interactions by restricting the carrying capacity of susceptible host cells. We further demonstrate that the replication threshold enables coexistence of susceptible and resistant bacteria in phage-treated mice, with implications for phage-based applications in complex environments like the gut.},
}

@article {pmid42890268,
year = {2026},
author = {Wei, Y and Yang, K and Lu, Q and Zhou, X and Huang, H and Liu, M and Wang, L and Shang, L and Peng, T and Zeng, X},
title = {Etiology-associated differences in the gut microbiome and metabolome in hepatocellular carcinoma: an exploratory study of alcohol-related and HBV-related cases.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1927595},
doi = {10.3389/fmicb.2026.1927595},
pmid = {42890268},
issn = {1664-302X},
abstract = {Hepatocellular carcinoma (HCC) arises in heterogeneous etiological contexts, but direct cross-omics comparisons between HCC subgroups defined by different etiologies remain limited. In this exploratory study, we combined fecal 16S rRNA gene sequencing and untargeted serum metabolomics with exploratory cross-omics analyses to compare gut microbial composition, serum metabolic profiles, and microbiome-metabolite association patterns between hepatitis B virus-related HCC (HBV-HCC) and alcohol-related HCC (ALD-HCC). Forty patients who underwent primary tumor resection were included, comprising 26 with HBV-HCC and 14 with ALD-HCC. Alpha diversity indices did not differ significantly between groups, whereas within-group Bray-Curtis dissimilarity was greater in ALD-HCC and genus-level beta-diversity ordination showed only modest separation between the two groups. LEfSe-based screening suggested the enrichment of candidate taxa, including Faecalibacterium, Roseburia, Lachnospira, Turicibacter, and Butyribacter in HBV-HCC, whereas Allisonella and Coprobacillus were enriched in ALD-HCC. Untargeted metabolomics showed group separation in supervised models and identified exploratory candidate metabolic features mainly involving glycerophospholipid metabolism, primary bile acid biosynthesis, aminoacyl-tRNA biosynthesis, and central carbon metabolism in cancer; however, these metabolite-level findings did not remain significant after multiple-testing correction. Procrustes and O2PLS analyses indicated limited global concordance between the microbiome and metabolome, although exploratory associations were observed between several phosphatidylcholine-related features and microbial taxa. Overall, HBV-HCC and ALD-HCC may be associated with different gut microbial and serum metabolic patterns, and these findings should be considered exploratory and hypothesis-generating.},
}

@article {pmid42890524,
year = {2026},
author = {Müller, JP and Friske, D and Hasoumi, M and Miller, B and Sarömba, JA and Tupiec, J and Koczera, P and Laurentius, T and Clavel, T and Stingl, JC and Just, KS},
title = {Solanidine metabolic ratios for CYP2D6 phenotyping after a standardized potato meal.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1886427},
doi = {10.3389/fphar.2026.1886427},
pmid = {42890524},
issn = {1663-9812},
abstract = {INTRODUCTION: The recent identification of the diet-derived CYP2D6 biomarker solanidine, a potato constituent, enables the study of CYP2D6 activity in vivo. Although solanidine metabolic ratios (MR) were shown to be relatively stable over the day with high positive correlations to CYP2D6 phenotype and genotype, the influence of a solanidine-containing potato meal on solanidine metabolite plasma concentrations and MR is unclear.

METHODS: In this study with 20 healthy participants, not preselected for specific CYP2D6 genotypes, a standardized potato meal was administered after 3 days of potato-fasting (DRKS00031441). Blood sampling was conducted at 0, 0.5, 1, 1.5, 2, 3, 4, 5 and 29 h. Participants were genotyped for CYP2D6 and plasma concentrations of solanidine and its metabolites 4-OH-solanidine and 3,4-secosolanidine-3,4-dioic acid (SSDA) were measured by LC-MS/MS. MRs were formed by dividing metabolite by substrate concentrations at each sampling time point.

RESULTS: Solanidine and metabolite plasma concentrations showed no consistent increases. Solanidine plasma concentrations (29 h vs. baseline) increased in median 0.09 ng/mL (range: -0.37 to 1.43 ng/mL). Within the period of 29 h, the linear relationship of solanidine ln MRs to the CYP2D6 activity score (AS) improved over time after intake of the potato meal with the best association after 29 h (r[2] = 0.56).

DISCUSSION: Changes in solanidine and metabolite plasma concentrations after the potato meal were variable, which could be attributed to interindividual absorption variability. CYP2D6 phenotyping may be improved by a previous potato meal at least 1 day before blood sampling. This may allow solanidine CYP2D6 phenotyping in populations with low dietary potato consumption.},
}

@article {pmid42890539,
year = {2026},
author = {Yao, H and Chen, J and Liu, C and Huang, J and Liu, L and Wang, Q and Wang, F},
title = {Structural and functional characterization of the gut microbiota in women with early pregnancy loss in Northwest China.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1895733},
doi = {10.3389/fmicb.2026.1895733},
pmid = {42890539},
issn = {1664-302X},
abstract = {BACKGROUND: Early pregnancy loss (EPL) is a common adverse pregnancy outcome with a complex and incompletely understood etiology. Moreover, metagenomic studies of the gut microbiota in women with EPL in Northwest China remain limited.

OBJECTIVE: This study aimed to characterize differences in gut microbial composition and predicted functional potential between women with EPL (EPL group) and normal controls (NCs) using shotgun metagenomic sequencing.

METHODS: We collected fecal samples from 216 women in Northwest China (EPL group, n = 72; NCs, n = 144). Shotgun metagenomic sequencing was performed to analyze gut microbiota composition and assess the functional potential of the microbiota.

RESULTS: Our study revealed significant differences in the composition of the gut microbiota between the EPL group and NCs, as assessed by alpha and beta diversity analyses (p < 0.001). Bacteroides was significantly more abundant in the EPL group, whereas Coprococcus, Bifidobacterium, and Roseburia were significantly more abundant in NCs. Compared to NCs, the EPL group had higher relative abundances of species such as Bacteroides stercoris, Bacteroides plebeius, and Bacteroides uniformis, but lower relative abundances of Bifidobacterium adolescentis, Megamonas funiformis, and Fusicatenibacter saccharivorans. Partial correlation analysis showed that Bacteroidetes was positively correlated with EPL at the phylum level. At the genus level, Odoribacter, Parabacteroides, and Haemophilus were positively correlated with EPL, whereas Corynebacterium, Lactobacillus, and Roseburia were negatively correlated with EPL. Metabolic pathway analysis revealed that pathways such as L-rhamnose degradation I, L-arginine biosynthesis III and 2-oxobutanoate degradation I exhibited significant positive correlations with EPL. In contrast, pathways including purine nucleobases degradation I (anaerobic) and chitin derivatives degradation showed significant negative correlations with EPL.

CONCLUSION: The results of our study revealed significant differences in gut microbiota composition and metabolic pathways between the EPL group and NCs, indicating that gut microbiome alterations are associated with EPL.},
}

@article {pmid42890700,
year = {2026},
author = {Sun, W and Xiao, M and Ali, SL and Jin, C and Khan, A and Shakirullah, and Ni, R and An, Y and Zhang, M and Tian, Y and Kaushik, S and Zhang, Y and Gong, W},
title = {Correction: Harnessing the gut microbiome to combat tuberculosis: a technological and clinical review.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1961302},
doi = {10.3389/fcimb.2026.1961302},
pmid = {42890700},
issn = {2235-2988},
abstract = {[This corrects the article DOI: 10.3389/fcimb.2026.1847443.].},
}

@article {pmid42890780,
year = {2026},
author = {Li, S and Kort, R and de Meij, TGJ and Brul, S and Wortel, MT and Westerhuis, JA},
title = {MicrobTiSDA: A flexible R package for inferring interspecies interactions and abundance dynamics in microbiome time-series data.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70067},
doi = {10.1002/imo2.70067},
pmid = {42890780},
issn = {2996-9514},
abstract = {MicrobTiSDA is a user-friendly and flexible R package specifically designed for longitudinal microbiome data analysis. By integrating process-oriented functional modules-including data input, data preprocessing, interspecies interaction inference, natural spline regression modeling, temporal pattern clustering, and random forest classification-MicrobTiSDA enables users to efficiently and systematically infer reliable interspecies interactions and accurately characterize microbial abundance dynamics from time-series data. The package is compatible with diverse experimental designs and provides comprehensive, intuitive visualizations, thereby substantially enhancing both the efficiency of longitudinal microbiome data analysis and the depth of biological interpretation.},
}

@article {pmid42890788,
year = {2026},
author = {Dai, Q and Cui, X and Gao, C and Tang, X and Wen, K and Shi, M and Zhang, C and Liu, Y and Yang, X and Huang, Q and Zhu, L},
title = {Sexual dimorphism in hormone-gut microbiome associations across reproductive states in wild giant pandas.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70108},
doi = {10.1002/imo2.70108},
pmid = {42890788},
issn = {2996-9514},
abstract = {Gut microbiota-host endocrine interactions in wild mammals remain poorly understood. Giant pandas experience seasonal dietary shifts and constrained annual reproduction, offering an ideal model to investigate microbiome-endocrine coupling. We integrated fecal hormone profiling, microsatellite-based individual identification, and gut microbiome sequencing in wild giant pandas. Microbial diversity and composition varied seasonally, with α diversity peaking during bamboo shoot-feeding. Hormonal dynamics followed predictable patterns: elevated estrogen during estrus, sustained progesterone post-estrus, and higher cortisol during leaf/stem-feeding periods. Hormone levels significantly correlated with microbial taxa and diversity, indicating coordinated microbiome-endocrine dynamics. Notably, microbiome-hormone coupling was significant in males but not in females, and males exhibited greater hormonal and microbial variability. Our findings demonstrate seasonal restructuring of gut microbiome and endocrine profiles in wild giant pandas with sex-dependent coupling, providing an integrated framework for non-invasive conservation monitoring.},
}

@article {pmid42890790,
year = {2026},
author = {Gui, Z and Su, H and Chen, Y and Yuan, J and Gao, Y and Yu, Z and Zhang, J and Zhu, Q and Gu, M and Du, M and Wang, Z and Chen, M},
title = {Ragomics-Meta: An open-source, scalable, reproducible, and extensible multi-omics analysis workflow.},
journal = {iMetaOmics},
volume = {3},
number = {3},
pages = {e70121},
doi = {10.1002/imo2.70121},
pmid = {42890790},
issn = {2996-9514},
abstract = {Ragomics-Meta is an open-source, scalable, and reproducible multi-omics workflow for metabolism-centered analysis (https://www.raganetwork.com/). It integrates scRNA/snRNA-seq, spatial transcriptomics, scATAC-seq, and metabolomics modules to support quality control, dimensionality reduction, clustering, differential expression and accessibility analyses, pathway activity scoring, cell-cell communication inference, transcription-factor network analysis, and spatial metabolism exploration. By incorporating established tools such as Scanpy, Seurat, Squidpy, COMMOT, SnapATAC2, MEBOCOST, scMetabolism, AUCell, and a curated gutMGene-based resource, Ragomics-Meta enables systematic characterization of tumor metabolic programs and host-microbiome interactions. AI-assisted interpretation further facilitates biological annotation and hypothesis generation, providing a user-friendly framework for integrative single-cell and spatial multi-omics analysis.},
}

@article {pmid42890796,
year = {2026},
author = {Lehosmaa, K and Koskimäki, JJ and Podolich, O and Ahonen, SHK and Ruotsalainen, AL and Wäli, PR and Greger, M and Rashid, U and Baruah, N and Edesi, J and Markkola, A and Kiani, S and Postila, H and Kujala, K and Ronkanen, AK and Pirttilä, AM},
title = {Aquatic moss precipitates metals in the presence of a specific endophytic microbiome.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70061},
doi = {10.1002/imo2.70061},
pmid = {42890796},
issn = {2996-9514},
abstract = {Harnessing moss-microbe interactions for metal removal. Schematic representation of aquatic moss Warnstorfia fluitans and its microbial symbionts in the remediation of metal-contaminated waters. Amplicon sequencing and advanced microscopy revealed microbial community composition and role of moss symbionts in metal accumulation within the moss tissues from mining-impacted and control sites. The moss efficiently accumulates metals, including iron, which is stored intracellularly near the cell membrane in association with endophytic microorganisms, and mosses in metal-rich environments host a distinct microbiome with reduced diversity compared to control. In metal-rich conditions, endophytic fungal species Phialocephala bamuru and Hyaloscypha hepaticola were abundant and cultivated, potentially contributing to metal tolerance or accumulation in the moss. These results suggest that W. fluitans along with its metal-tolerant microbial symbionts offers exciting potential for innovative nature-based purification systems for metal-contaminated waters.},
}

@article {pmid42890816,
year = {2026},
author = {Peng, O and Liu, Y and Wang, X and Huang, Y and Yang, Y and Kang, Q and Geng, R and Hu, G and Lv, A and Hu, F and Xia, Y and Luo, X and Liao, J and He, Y and Kuang, Z and Du, Y and Zhang, Y and Xue, C and Han, Z and Li, WJ and Dong, L and Zhang, H and Cao, Y},
title = {Akkermansia muciniphila enhances chicken resistance to infectious bronchitis virus by boosting GABA synthesis and suppressing the NF-κB inflammatory pathway.},
journal = {iMetaOmics},
volume = {3},
number = {1},
pages = {e70086},
doi = {10.1002/imo2.70086},
pmid = {42890816},
issn = {2996-9514},
abstract = {Infectious bronchitis virus (IBV) is a major viral pathogen causing substantial economic losses in the global poultry industry. However, the limited efficacy of commercial vaccines and the absence of approved antiviral drugs underscore the urgent need for novel strategies to combat IBV, particularly in the context of antibiotic-free poultry production. Emerging evidence suggests that gut microbiota plays a crucial role in shaping host immunity and antiviral resilience. In this study, we demonstrated that gut microbiota composition is a key determinant of IBV resistance in chickens, as revealed through a fecal microbiota transplantation (FMT) model. Utilizing multi-omics approaches, we conducted a comprehensive characterization of microbiomic, viromic, and metabolic differences among adult chickens, young chickens, and FMT-treated young chickens for the first time, establishing a mechanistic link between gut microbiota and IBV resistance. Building on these insights, longitudinal microbiome profiling in a newly developed persistent IBV infection model identified Akkermansia muciniphila as the key bacterium conferring IBV resistance, with its administration improving survival rates from 30-35% to 90-95%. Additionally, two novel candidate probiotics, Cloacibacillus porcorum and Neglecta timonensis, exhibited moderate yet measurable protective effects. Mechanistic investigations revealed that Akkermansia muciniphila enhances γ-aminobutyric acid (GABA) production, which suppresses NF-κB-driven inflammatory responses, reduces pro-inflammatory cytokine levels, alleviates nephritis, and upregulates antiviral interferon expression, thereby fortifying host defenses against IBV infection. These findings provide a scientific foundation for deploying live biotherapeutic products as an intervention strategy against IBV and highlight the broader potential of gut microbiota modulation in mitigating infectious diseases and optimizing poultry health management.},
}

@article {pmid42878649,
year = {2026},
author = {Fansler, RT and Zhu, W},
title = {Small RNAs as emerging regulators of commensal adaptation in the mammalian gut.},
journal = {Infection and immunity},
volume = {},
number = {},
pages = {e0029226},
doi = {10.1128/iai.00292-26},
pmid = {42878649},
issn = {1098-5522},
abstract = {The commensal bacteria of the intestinal microbiota inhabit one of the most densely populated and dynamic microbial ecosystems known, where fluctuations in nutrient availability, host-derived stresses, and microbial competition require highly coordinated regulatory responses to maintain colonization and fitness. As a stable, homeostatic microbiota performs essential functions for the host, understanding how commensals adapt to the fluctuating intestinal environment is important for maintaining intestinal homeostasis and informing the development of new microbiota-targeted therapeutics. Throughout diverse bacterial species, rapid adaptation to environmental perturbations is mediated in part by small regulatory RNAs (sRNAs). While most sRNA research has focused on a limited number of model organisms, particularly bacterial pathogens, recent studies have uncovered important roles for these noncoding RNAs in promoting the fitness and resilience of gut commensals. Advances in differential RNA sequencing, comparative genomics, and functional genetics have revealed diverse repertoires of sRNAs in prominent gut symbionts, with regulatory roles in nutrient acquisition, stress responses, and host colonization. This minireview highlights recent advances and outlines future directions to further elucidate sRNA-mediated regulation as a pillar of commensal resilience in the mammalian gut.},
}

@article {pmid42878705,
year = {2026},
author = {Keuschnig, C and Feord, H and Broadwell, ELM and Zervas, A and Tranter, M and Anesio, AM and Benning, LG},
title = {Aerobic anoxygenic phototrophs are widespread and active members of Greenland Ice Sheet microbiomes.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag116},
pmid = {42878705},
issn = {1574-6941},
abstract = {The Greenland Ice Sheet (GrIS) hosts diverse microbial communities where glacier ice algae, snow algae, and cyanobacteria act as key primary producers across bare ice, snow, and cryoconite habitats, yet the ecological roles of associated heterotrophic prokaryotes remain poorly understood. Aerobic anoxygenic phototrophs (AAPs), known to couple light harvesting to heterotrophy and enter trophic relationships with algae in marine systems, suggesting they may represent an important but underexplored functional group in supraglacial ecosystems. Using genome-resolved analyses of supraglacial metagenomes and metatranscriptomes from Greenland, we recovered nine AAP metagenome-assembled genomes (MAGs) (4% of the 229 recovered MAGs) consistently enriched in bare ice and cryoconite communities, but nearly absent in snow. A meta-analysis of 2 451 public metagenomes supported this cryospheric habitat association. AAP_MAGs were disproportionally enriched in thiosulfate oxidation and bicarbonate-dependent carbon assimilation pathways relative to other MAGs. Iron and CO oxidation pathways were broadly distributed across the GrIS microbiome, including in AAPs, together suggesting adaptation strategies in supraglacial ecosystems. Genomic evidence for algal coupling via sulfoquinovose degradation was limited. Overall, we document that AAPs are active and widespread in weathering crust habitats, highlighting their potential contributions to biogeochemical cycling in supraglacial ecosystems.},
}

@article {pmid42879303,
year = {2026},
author = {Ahearn-Ford, S and Aboklaish, A and Young, GR and Lowe, J and Masi, AC and Gallacher, D and Marchesi, JR and Berrington, JE and Kotecha, S and Stewart, CJ},
title = {The impact of prophylactic azithromycin on the developing preterm gut microbiome and resistome.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2748147},
doi = {10.1080/19490976.2026.2748147},
pmid = {42879303},
issn = {1949-0984},
mesh = {Humans ; *Azithromycin/administration & dosage ; *Anti-Bacterial Agents/administration & dosage ; Infant, Newborn ; *Infant, Premature/growth & development ; *Gastrointestinal Microbiome/drug effects ; Double-Blind Method ; Drug Resistance, Bacterial ; *Bacteria/genetics/drug effects/classification/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Female ; *Antibiotic Prophylaxis ; Probiotics/administration & dosage ; Male ; },
abstract = {Early-life antibiotic exposure can profoundly impact the developing preterm gut microbiome and resistome, with short- and long-term consequences for health. In a large multi-center (n = 28) study of 693 preterm infants, we investigated the effects of 10 d of prophylactic intravenous azithromycin on the gut microbiome and antibiotic resistance genes (ARGs). The AZithromycin ThErapy for Chronic Lung Disease of Prematurity (AZTEC) study was a double blind, randomized, placebo-controlled trial of preterm infants (born < 30 weeks of gestation), treated from birth for 10 d with either intravenous azithromycin or placebo, and sampled longitudinally for 21 d or discharge. Using 16S rRNA gene sequencing, antibiotic susceptibility testing, and quantitative PCR, we show azithromycin reduced microbial diversity and the relative abundance of health-associated Bifidobacterium and increased relative abundances of pathobionts Staphylococcus and Enterobacter/Klebsiella. This early azithromycin treatment increased the number of macrolide-resistant genes, including the presence of erm (C), which persisted for the duration of the study. Probiotic use (at individual unit discretion) increased alpha diversity and Bifidobacterium relative abundance, but did not fully mitigate the effects of azithromycin receipt. Combined azithromycin and probiotics further increased the enrichment of Enterobacter/Klebsiella and total ARGs, including erm(C). These findings highlight the impacts of antibiotic and probiotic use, both important in balancing infection control issues and microbiome disruption and antimicrobial resistance.},
}

Humans
*Azithromycin/administration & dosage
*Anti-Bacterial Agents/administration & dosage
Infant, Newborn
*Infant, Premature/growth & development
*Gastrointestinal Microbiome/drug effects
Double-Blind Method
Drug Resistance, Bacterial
*Bacteria/genetics/drug effects/classification/isolation & purification
RNA, Ribosomal, 16S/genetics
Female
*Antibiotic Prophylaxis
Probiotics/administration & dosage
Male

@article {pmid42879678,
year = {2026},
author = {Lin, ZR and Shi, JC and Qiu, CC and Wu, ZX and Lin, XQ and He, GQ and Liu, SD and Du, QW and Lin, HB and Wu, LP and Sun, F and Jiang, XG},
title = {Metagenomic insights into the pulmonary microbiome of drug-sensitive and multidrug-resistant tuberculosis patients.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2720327},
doi = {10.1080/07853890.2026.2720327},
pmid = {42879678},
issn = {1365-2060},
mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Microbiota/genetics ; *Tuberculosis, Multidrug-Resistant/microbiology/drug therapy ; Female ; Male ; Metagenomics ; *Lung/microbiology ; Middle Aged ; Adult ; Prospective Studies ; Antitubercular Agents/therapeutic use/pharmacology ; },
abstract = {BACKGROUND: While the pulmonary microbiota may influence TB pathogenesis, direct comparisons between drug-sensitive (DS-TB) and multidrug-resistant (MDR-TB) patients remain scarce. This study explored microbiome differences between these groups.

METHODS: Bronchoalveolar lavage fluid (BALF) from 30 prospective patients (11 DS-TB, 19 MDR-TB) was analysed via metagenomic sequencing.

RESULTS: Patients with MDR-TB showed lower α-diversity and distinct β-diversity compared with patients with DS-TB. Streptococcus and Prevotella were relatively enriched in DS-TB, whereas Staphylococcus, Cutibacterium, and Mycobacterium were more abundant in MDR-TB. DS-TB showed enrichment of 45 carbohydrate-active enzyme families and core metabolic annotations, whereas MDR-TB showed enrichment of infection- and immunity-related functional annotations and a less connected taxonomic network. An exploratory random forest analysis identified six candidate genera and yielded an internally cross-validated AUC of 0.957.

CONCLUSIONS: MDR-TB was associated with lower pulmonary microbial diversity, altered community composition, and shifts in predicted microbial functions. These findings characterise lower-airway microbiome differences between DS-TB and MDR-TB and provide a basis for further validation.},
}

Humans
Bronchoalveolar Lavage Fluid/microbiology
*Microbiota/genetics
*Tuberculosis, Multidrug-Resistant/microbiology/drug therapy
Female
Male
Metagenomics
*Lung/microbiology
Middle Aged
Adult
Prospective Studies
Antitubercular Agents/therapeutic use/pharmacology

@article {pmid42879794,
year = {2026},
author = {Beck, EA and Smith, CA and Currey, MC and Small, CM and Bohannan, BJM and Cresko, WA},
title = {Spontaneous hypopigmentation mutant in threespine stickleback fish exhibits changes in the gut microbiome consistent with inflammatory bowel diseases.},
journal = {G3 (Bethesda, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1093/g3journal/jkag284},
pmid = {42879794},
issn = {2160-1836},
abstract = {Albinism is a large group of disorders characterized by a loss of pigment in ectoderm-derived tissues - most noticeably impacting the skin, hair, and eyes. Albinism is categorized as either syndromic or non-syndromic. Syndromic albinisms include a wide range of disorders with mutations impacting not just pigmentation but other cellular functions. These include, non-exclusively, melanogenesis disorders, endosome trafficking disorders like lysosomal storage disorders, and cell migration disorders. Mutations leading to syndromic albinisms can cause multi-organ system symptoms due to broad disruption lysosome related organelles (LROs) function. Various genetic mutations impact biogenesis, cell maturation, or trafficking at different stages which can lead to a range of severity. Syndromic albinisms also present with different combinations of symptoms depending on the impacted organelles; including oculocutaneous albinism (OCA) (melanosomes), blood diathesis (platelet dense granules), pulmonary fibrosis (lamellar bodies), or chronic inflammation (multiple cellular sources). Animal models for these multisymptomatic complex disorders are needed to understand the effects on systemic health. One such area of interest is in gut health of those with syndromic albinism. Shared inflammatory patterns of syndromic albinisms like Hermansky-Pudlak Syndromes (HPS) and Inflammatory Bowel Disease (IBD) are well studied, with animal models of HPS jointly used to study patterns of inflammation in IBD. However, the impact of this shared gastrointestinal inflammation on the gut microbiome remains unexplored. Using a spontaneously identified mutant family of threespine stickleback fish, we characterize phenotypes consistent with oculocutaneous albinism and vision impairment and demonstrate shared features of gut health to IBD extend from inflammation to the gut microbiome. We argue syndromic albinism models should be explored as models to study the gut microbiome in addition to inflammatory phenotypes in IBD, and importantly, be used to test microbial/dietary interventions for both IBD and syndromic albinisms.},
}

@article {pmid42879796,
year = {2026},
author = {Vicente-Díez, I and Mooney, KA and Vázquez-González, C},
title = {Contrasting effects of native soil microbiomes on direct and indirect herbivore resistance in a dominant shrub species.},
journal = {Annals of botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/aob/mcag334},
pmid = {42879796},
issn = {1095-8290},
abstract = {BACKGROUND AND AIMS: The soil microbiome is known to modulate plant resistance to insect herbivores. Research on this topic has traditionally focused on bottom-up effects of plants on insects (direct resistance). However, how soil microbiomes affect plant resistance via top-down control of insects by natural enemies (indirect resistance) remains understudied. We conducted a greenhouse experiment using Baccharis salicifolia as a model to test the effects of native soil microbiomes on (i) direct resistance against the generalist aphid Aphis gossypii and (ii) indirect resistance by natural enemies.

METHODS: We grew B. salicifolia plants in a common sterilized substrate that was either inoculated with 10% native field soil or left uninoculated as a sterile control and performed a bioassay with A. gossypii to assess direct resistance by measuring aphid performance (age at first reproduction and reproductive rate). Then, we assessed indirect resistance by excluding natural enemies and estimating effects on aphid colony size in plants growing in inoculated vs. uninoculated soil.

KEY RESULTS: Plants in inoculated soil exhibited a 15% increase in growth, while aphid reproduction was reduced by 18% compared to uninoculated soil. Moreover, soil inoculation significantly altered the strength of top-down control by natural enemies. Access to natural enemies reduced aphid colony size by 23% in uninoculated soils but only by 11% in inoculated soils, indicating weaker indirect resistance under soil inoculation.

CONCLUSIONS: We show that native microbial communities regulate plant-insect-natural enemy interactions via contrasting effects on direct and indirect resistance, underscoring the need to consider both pathways to understand microbial impacts on plant resistance.},
}

@article {pmid42879892,
year = {2026},
author = {Muoghalu, C and Sun, Z and Guo, J and Kaboggoza, HC and Lubwama, I and Manga, M},
title = {Effects of substrate moisture content on physiological development, performance, and gut microbiome of black soldier fly larvae during swine waste treatment.},
journal = {Waste management (New York, N.Y.)},
volume = {227},
number = {},
pages = {115924},
doi = {10.1016/j.wasman.2026.115924},
pmid = {42879892},
issn = {1879-2456},
abstract = {Black soldier fly larvae (BSFL) composting is a sustainable approach for treating swine waste. BSFL's performance depends on its digestive enzyme activity, which is shaped and enhanced by the gut microbiome. Moisture content influences gut microbiome composition and function; however, it is often overlooked, and its role remains poorly understood. We evaluated the effects of three moisture levels (65%, 75%, and 85%) on the larval gut microbiome, digestive enzyme activity, larval growth, protein content, and contaminant removal. Microbial communities in larval guts and substrates were characterized using 16S rRNA sequencing and multivariate analyses. Larvae reared at 65% moisture had the highest protein content (40.8% DM) and achieved significantly greater reductions in total organic carbon (85.4%), total nitrogen (47.9%), and total phosphorus (47.7%) than those reared at higher moisture levels. However, protease activity was highest at 75% moisture and alpha-amylase activity was highest at 85% moisture. Linear discriminant analysis effect size identified a more functionally enriched gut microbiome at 65% moisture, characterized by taxa associated with organic matter degradation, including Bacillaceae, Paenibacillaceae, and Caryophanaceae, and genera such as Paenibacillus, Peribacillus, and Stenotrophomonas, whereas higher moisture levels favored anaerobic and fermentative taxa. Spearman correlation analysis further identified associations between specific bacterial genera and enzyme activities, including a strong positive association between Enterococcus (enriched at 85% moisture) and alpha-amylase activity (ρ = 0.90). This study contributes to optimizing BSFL-based waste management and highlights the need for microbial enhancement strategies and research on antimicrobial resistance.},
}

@article {pmid42879932,
year = {2026},
author = {Medriano, CA and Chow, KW and Oh, JY and Bae, S},
title = {Weathering chemistry shapes the gut microbiome-metabolome-transcriptome response of adult zebrafish to aged polyethylene microplastics.},
journal = {Journal of hazardous materials},
volume = {518},
number = {},
pages = {143884},
doi = {10.1016/j.jhazmat.2026.143884},
pmid = {42879932},
issn = {1873-3336},
abstract = {Microplastics (MPs) in aquatic environments undergo continuous weathering, yet most toxicological studies still rely on pristine commercial particles, leaving biological consequences of distinct aging chemistries poorly resolved. Here, polyethylene (PE) MPs were aged through oxidative and hydrolytic pathways (UV+H2O, H2SO4, HNO3, and NaOH), characterized by FTIR (Fourier Transform Infrared Spectroscopy) and SEM (Scanning Electron Microscopy), and administered to zebrafish to link surface chemistry with the multilayered gut microbiome, metabolome, and host transcriptome responses. Weathering chemistry governed surface oxidation and morphological damage, with strong-acid treatment (H2SO4 ≫ HNO3) causing the most severe fragmentation. These surface differences propagated into chemistry-specific effects: an abundance-driven restructuring of the gut microbiota, including suppression of the core commensal Cetobacterium under alkaline aging and expansion of stress-tolerant environmental taxa; weathering-specific remodeling of the metabolome (NAD[+]/nicotinamide and glycosphingolipid); and low but treatment-specific transcriptional changes (6-13 DEGs per treatment, including a shared ∼800-fold induction of lhfpl5b under NaOH and UV+H2O). Multi-omics integration resolved into three chemistry-specific cross-omics axes, with the metabolome and transcriptome showing the strongest cross-layer concordance (Procrustes 1-M[2] = 0.38, p < 0.01). Weathered MPs from different degradation pathways cannot be aggregated into a single "aged-MP" category, as their hazards are chemistry-specific at every molecular layer.},
}

@article {pmid42880058,
year = {2026},
author = {Li, D and Yin, J and Zhou, H and Ge, N and Wang, B and Wang, T},
title = {Integrative multi-omics analysis reveals the PFAS-gut microbiome-FN1 axis in chronic kidney disease: From exposome to therapeutic target.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 2},
pages = {109478},
doi = {10.1016/j.compbiolchem.2026.109478},
pmid = {42880058},
issn = {1476-928X},
abstract = {Per- and polyfluoroalkyl substances (PFAS) are persistent environmental pollutants associated with chronic kidney disease (CKD), yet the molecular mechanisms linking PFAS exposure to renal fibrosis remain incompletely understood. We developed a Chemical-Microbiome-Metabolite-Target-Pathway-Disease (C-M-M-T-P-D) network framework integrating differential expression analysis of real GEO transcriptomic data (GSE104954, n = 195 kidney biopsies), gene set enrichment analysis across four pathway databases, two-sample Mendelian randomization with four complementary methods, molecular docking and molecular dynamics simulation of deoxycholic acid (DCA) to fibronectin 1 (FN1), and transcription factor and protein-protein interaction network analyses. FN1 was significantly upregulated in CKD (log2FC = 0.322, FDR = 6.67e-11), accompanied by elevated COL1A2, VIM, and POSTN, whereas TGFBR3 was downregulated (log2FC = -0.746, FDR = 1.67e-14). GSEA identified ECM-receptor interaction (NES = 2.23), interferon gamma response (NES = 2.70), and epithelial-mesenchymal transition (NES = 1.99) as top enriched pathways. MR analysis using real MiBioGen and CKDGen GWAS data (19 SNPs for Akkermansia, 12 SNPs for Desulfovibrio) revealed contrasting findings: Akkermansia to CKD showed no significant genetic association (0/4 methods, all p > 0.30), whereas Desulfovibrio to CKD demonstrated a robust positive genetic association across all four methods (IVW p = 0.008, WM p = 4.70e-04, MR-RAPS p = 1.46e-05, MR-cML p = 2.08e-06), though the significant Egger intercept (p = 0.005) for Desulfovibrio warrants cautious interpretation regarding pleiotropy. Molecular docking and 15-ns MD simulation confirmed stable DCA binding to FN1 (PDB: 2CG7, 1.20 A X-ray; MM/GBSA ΔGbind = -32.4 kcal/mol). The C-M-M-T-P-D network positioned FN1 as the third highest-degree node, bridging metabolite and pathway layers. This integrative multi-omics analysis provides multi-omics evidence supporting the PFAS-gut microbiome-FN1 axis as a hypothesis-generating framework for understanding CKD pathogenesis, supported by transcriptomic, structural, and network-level evidence, with genetic associations warranting further experimental validation.},
}

@article {pmid42880079,
year = {2026},
author = {Cha, HE and Jeon, AJ and Cho, HS and Lee, JW and Seo, J and Lee, S and Lim, SK},
title = {Age-associated variation in the Korean salivary microbiome: Exploratory assessment of spousal cohabitation as a potential confounder for forensic inference.},
journal = {Legal medicine (Tokyo, Japan)},
volume = {87},
number = {},
pages = {103038},
doi = {10.1016/j.legalmed.2026.103038},
pmid = {42880079},
issn = {1873-4162},
abstract = {The salivary microbiome reflects host physiology and environmental exposures and may provide complementary information for forensic trace interpretation. This study primarily investigated age-associated variation in salivary microbiome profiles from 182 Korean adults and secondarily explored reported spousal cohabitation as a potential contextual variable and source of confounding through ecological analyses and exploratory machine-learning approaches. An XGBoost regression model yielded a test-set mean absolute error of 7.49 years (R[2] = 0.31) for chronological age. Alpha diversity differed across age groups, and Bray-Curtis community composition varied modestly by age group (R[2] = 0.037). Binary classification of participants in their 20s and 30s versus those in their 40s and 50s achieved an accuracy of 0.741 and an area under the receiver operating characteristic curve of 0.76. For reported spousal cohabitation, an unadjusted exploratory analysis showed a small difference in community composition (R[2] = 0.012). However, in a multivariable marginal PERMANOVA including chronological age, sex, and cohabitation status simultaneously, age remained significantly associated with community composition (R[2] = 0.014, p = 0.0119), whereas cohabitation was not (R[2] = 0.004, p = 0.6898). This association also remained non-significant in a sensitivity analysis restricted to participants in their 30s-50s. These findings support a modest, distributed age-related signal, whereas the weaker cohabitation-associated pattern may partly reflect demographic confounding. This study extends limited population-specific evidence on age-associated salivary microbiome variation in Korean adults and supports further evaluation of salivary microbiome profiles as complementary, rather than stand-alone, forensic information requiring external validation, rigorous confounder control, and casework-relevant testing.},
}

@article {pmid42880184,
year = {2026},
author = {Erreygers, I and Pinedo-Bardales, M and Dey, H and Segata, N and Wittouck, S and Lebeer, S and Heidrich, V},
title = {Transmission of lactic acid bacteria: a case study of the human vaginal microbiome.},
journal = {Current opinion in microbiology},
volume = {94},
number = {},
pages = {102845},
doi = {10.1016/j.mib.2026.102845},
pmid = {42880184},
issn = {1879-0364},
abstract = {Lactic acid bacteria (LAB) are among the microorganisms to which humans are most frequently exposed, largely via consumption of fermented foods and probiotics and through interpersonal contact. Such continued exposure to LAB does not necessarily result in stable engraftment, raising fundamental questions about which factors mediate successful LAB transmission and niche specialization across human-associated microbiomes. Here, we rethink transmission of LAB across the human life course, spanning food-associated, within-host, and interindividual routes, highlighting that LAB transfer can occur across multiple contexts, but long-term engraftment depends less on exposure and more on host-mediated selection. As a paradigmatic case study, we present the human adult vaginal microbiome, a low-diversity environment generally dominated by strains of specific Lactobacillus species. These strains display clear signatures of niche specialization in the vaginal environment, making them taxonomically and functionally distinct from other LAB, and illustrating how host-mediated selection rather than exposure alone determines which LAB persist. This proposed conceptual framework, combined with the experimental and computational tractability of LAB, enables a better understanding of LAB engraftment in the human host, contributing to improved design and strain-level efficacy assessment of microbiome-based interventions, including probiotics, live biotherapeutic products, and microbiota transplants.},
}

@article {pmid42880228,
year = {2026},
author = {Corral, D and Belkaid, Y},
title = {Milking the niche: Microbial control of neonatal hematopoiesis.},
journal = {Cell},
volume = {189},
number = {21},
pages = {6561-6563},
doi = {10.1016/j.cell.2026.09.010},
pmid = {42880228},
issn = {1097-4172},
mesh = {Animals ; *Hematopoiesis ; Humans ; *Microbiota ; *Osteopontin/metabolism ; *Milk/immunology/microbiology ; Dendritic Cells/immunology ; },
abstract = {In this issue of Cell, Howard et al. reveal how the milk glycoprotein osteopontin shapes the neonatal microbiome to regulate hematopoiesis, promoting dendritic cell development and protection from severe respiratory infection. These findings uncover a maternal milk-microbiota pathway linking early-life nutrition to immune development and long-term disease susceptibility.},
}

Animals
*Hematopoiesis
Humans
*Microbiota
*Osteopontin/metabolism
*Milk/immunology/microbiology
Dendritic Cells/immunology

@article {pmid42880254,
year = {2026},
author = {Meyers, M and Medina Evora, G and Molina Tijeras, JA and Brauer, M and Benzarti, M and Jans, M and Delgado, LF and Schorr, L and Rodriguez, F and Ternes, D and Ouyang, KS and Moskal, K and Schlicker, L and Tsenkova, M and Lucchetti, M and Gilson, C and Gabola, M and Carpentier, A and Nuciforo, PG and Koncina, E and Pozdeev, VI and Vereecke, L and Wilmes, P and Puschhof, J and Letellier, E},
title = {Gemella morbillorum promotes colorectal tumorigenesis through barrier disruption and invasion-dependent DNA damage.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.09.016},
pmid = {42880254},
issn = {1934-6069},
abstract = {Bacteria are increasingly recognized as contributors to cancer, yet the underlying mechanisms remain unclear for most species. Here, we find that Gemella morbillorum (Gm) is enriched in feces and tumor tissues from patients with colorectal cancer (CRC) and reveal a multi-step host-pathogen mechanism that promotes colorectal tumorigenesis. In mouse models of CRC, Gm suppresses IL-22 production by type 3 innate lymphoid cells (ILC3s), impairing intestinal barrier function and facilitating bacterial translocation to early neoplastic lesions. At the tumor site, Gm utilizes an ANXA2-dependent, clathrin-mediated pathway to invade CRC cells. Gm induces profound lipid remodeling, characterized by the accumulation of oxidation-prone fatty acids and enhanced lipid peroxidation, which contributes to invasion-dependent DNA damage. Inhibition of lipid peroxidation attenuates Gm-induced DNA damage, functionally linking lipid oxidative stress to genotoxicity. Together, these findings identify Gm as a candidate onco-pathogen in CRC that uses multiple mechanisms to disarm the intestinal barrier and trigger genotoxicity.},
}

@article {pmid42880376,
year = {2026},
author = {Yu, Q and Zhang, Z and Tian, Z and Kuang, J and Corbin, KD and Oberlin, LE and Collins, A and Goodpaster, BH and Erickson, KI and Owen, N and Dunstan, DW and Hillman, CH and Kramer, A and Liu-Ambrose, T and Lowe, C and Heath, M and Moon, HY and Banks, WA and Paas, F and Feter, N and Raichlen, DA and Kelley, KW and Allen, JM and Herold, F and Zou, L},
title = {Sedentary behavior as a Gut-Brain metabolic state.},
journal = {Brain, behavior, and immunity},
volume = {},
number = {},
pages = {107068},
doi = {10.1016/j.bbi.2026.107068},
pmid = {42880376},
issn = {1090-2139},
abstract = {Sedentary behavior (SB) is prevalent in daily life, with a growing number of studies reporting that higher SB exposure is associated with poorer cardiometabolic and brain health. Thus, in line with a broader paradigm shift, SB should be considered as a postural and low-contractile metabolic state, shaped by both total exposure and bout patterning, that is related to, but distinct from, physical activity (PA), rather than simply the absence of the latter. Regarding the gut microbiome, current evidence on the role of SB remains limited and indirect, as human studies have not yet experimentally manipulated the SB exposure. To generate novel, yet testable hypotheses on the role of SB on the gut microbiome and brain health, this article synthesizes the current evidence base by emphasizing limitations related to cross-sectional designs, measurement heterogeneity, potential confounding by diet, sleep, medications, and PA, and the absence of established quantitative thresholds for SB exposure. Building on broader microbiome, metabolic, inflammatory, and gut-brain axis literature, we outline candidate pathways through which SB exposure, especially prolonged uninterrupted sitting, may alter microbe-derived metabolites and host responses, focusing on short-chain fatty acids, bile acid signaling, and tryptophan-derived metabolism alongside barrier-immune activation and autonomic-vagal circuitry relevant for brain health. Thus, this review extends prior SB-brain health frameworks by positioning SB as a specific gut-brain metabolic state with potential unique effects on a range of brain health-related outcomes. To probe the prediction that changes in SB patterns can affect gut-derived metabolites and specific brain health domains, suitable study designs are discussed. More specifically, future studies should combine accurate measures of SB and PA exposure with gut microbiome and blood-based metabolite assessments, vascular and inflammatory markers, autonomic measures, and standardized tests of cognition and mood, collected at different times, such as after meals and across the day, to better quantify and understand temporal dynamics. Approaching the gut-brain axis by isolating the effects of SB exposure is likely to generate practically relevant and impactful insights that not only help to inform stakeholders, such as policymakers, but also provide the basis for more fine-grained lifestyle recommendations to preserve and improve brain health.},
}

@article {pmid42880461,
year = {2026},
author = {Mitrea, L and Calinoiu, LF and Martau, GA and Teleky, BE and Cocean, AM and Odocheanu, R and Stefanescu, BE and Vodnar, DC},
title = {From Gut Microbiome to Aging Brain: Butyrate as a Neurogeroscience Effector.},
journal = {Neuroscience and biobehavioral reviews},
volume = {},
number = {},
pages = {107037},
doi = {10.1016/j.neubiorev.2026.107037},
pmid = {42880461},
issn = {1873-7528},
abstract = {Aging-related cognitive decline is increasingly linked to disruption of the microbiome-gut-brain axis, in which age-associated dysbiosis progressively reduces butyrate production, a short-chain fatty acid and central neuroactive metabolite generated by bacterial fermentation of dietary fiber. Experimental studies indicate that butyrate can influence multiple processes relevant to brain aging, including histone deacetylase activity, neuroinflammatory signaling, microglial phenotypes, blood-brain barrier integrity, synaptic plasticity, and neurogenesis. Through these mechanisms, butyrate may modulate several molecular and cellular processes involved in brain aging, although evidence for direct causal effects in the human brain remains limited. Preclinical studies report neuroprotective effects across several models of aging and neurological disease; however, direct evidence in humans remains limited and largely associative or indirect. Therefore, this review critically synthesizes current evidence on microbiome-derived butyrate in brain aging, encompassing its microbial production and age-related alterations, molecular and cellular mechanisms, associations with neurodegenerative and neuropsychiatric conditions, and emerging strategies for therapeutic modulation and delivery. It examines emerging biotechnological strategies - including prodrug design, nanoparticle- and liposomal-based delivery systems, gut-targeted formulations, and microbiome engineering - all developed to overcome the blood-brain barrier and restore therapeutically relevant butyrate concentrations in the aging brain. By bridging fundamental microbiome biology and translational neuroscience, this review positions butyrate as a mechanistically grounded neurogeroscience effector and charts a roadmap for its application in promoting brain health across the aging continuum.},
}

@article {pmid42880574,
year = {2026},
author = {Wei, Q and Wu, J and Kang, W and Xu, S and Han, B},
title = {Laboratory larval exposure to mixed-size polystyrene micro/nanoplastics disrupts lipid metabolism and reshapes the hemolymph metabolome and gut microbiota of adult honeybee workers.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129347},
doi = {10.1016/j.envpol.2026.129347},
pmid = {42880574},
issn = {1873-6424},
abstract = {Micro/nanoplastics are pervasive contaminants in terrestrial ecosystems, yet their developmental toxicity to pollinators remains insufficiently understood. Here, worker larvae of the honeybee (Apis mellifera) were orally exposed under controlled laboratory conditions to a mixed-size polystyrene micro/nanoplastic (PS-MNP) system containing 50 nm, 100 nm, and 5 μm particles at a 1:1:1 mass ratio across 1-500 mg/L. Survival was assessed using 48 larvae per group, and adult hemolymph metabolomics and gut microbiome analyses were conducted for adults derived from the 10 mg/L larval exposure group using six biological replicates per treatment. Larval PS-MNP exposure reduced survival, transiently increased larval body mass, and disrupted nutrient allocation, as reflected by decreased total protein and free fatty acids but increased glycogen and triglyceride. In the larval fat body, PS-MNPs induced oxidative stress and lipid droplet accumulation, accompanied by transcriptional changes consistent with enhanced lipid storage and impaired lipophagy. These developmental disturbances were followed by post-metamorphic effects. Newly emerged workers exhibited midgut injury and oxidative imbalance. Moreover, adults derived from exposed larvae displayed pronounced hemolymph metabolomic reprogramming and altered gut microbiota after colony reintroduction. More than 1,200 differential hemolymph metabolites were detected, with downregulated features enriched mainly in lipid-remodeling, eicosanoid-related, and autophagy-associated pathways. The adult gut microbiota showed depletion of Gilliamella apicola and Bartonella apis and enrichment of Lactobacillus apis and Frischella perrara. Collectively, these findings show that larval-only exposure to a mixed-size PS-MNP system can disturb developmental lipid/redox homeostasis and be followed by intestinal, hemolymph metabolic, and gut microbial alterations after metamorphosis. This integrated cross-stage evidence advances understanding of micro/nanoplastic developmental ecotoxicology in beneficial terrestrial insects and provides evidence for considering developmental windows in future pollinator risk assessment.},
}

@article {pmid42880617,
year = {2026},
author = {Chen, S and Xiao, Q and Liu, X and Jiang, J and Lei, W and Zhang, S and Zeng, Y and Liu, J and Li, J and Xie, Y and Hu, H and Chen, S and Rong, F and Cai, S},
title = {Development of a novel diagnostic tool for community-acquired pneumonia based on microbial community characteristics.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {},
number = {},
pages = {106011},
doi = {10.1016/j.meegid.2026.106011},
pmid = {42880617},
issn = {1567-7257},
abstract = {BACKGROUND: The lung microbiota plays a key role in pneumonia. A correct diagnosis in the early stage helps treatment and limits severity progression of community-acquired pneumonia (CAP).

METHODS: There were 42 patients with CAP and 20 controls. Amplicon bacterial 16S sequencing from bronchoalveolar lavage fluid samples revealed indicator genera by linear discriminant analysis effect size, random forest and ROC analyses. The abundance of bacteria was combined with laboratory inflammatory indexes to construct logistic regression models for CAP diagnosis. The final predictive model with a lower Akaike information criterion (AIC) was internally validated by bootstrap resampling.

RESULTS: After confirming lower respiratory tract (LRT) microbiome dysbiosis in CAP patients, we identified five indicator genera: Moraxella (M), Prevotella_1 (P), Lautropia (L), Neisseria (N), and Fusobacterium (F). Their combined effect was incorporated by calculation of the joint prediction probability (PRE) based on their relative abundances as PRE = 1 / (1 + EXP (-4.39 + 18.96 M + 9.30P - 5.38 L + 0.89 N + 0.70F)). A nomogram was constructed for CAP diagnosis that incorporated PRE with serum levels of CRP (cut-off ≥5.23 mg/L) and Neutrophil % (cut-off ≥66.05%). After internal validation, this nomogram showed satisfactory diagnostic performance with the bootstrap-corrected AUC of 0.927 and a well-fitting calibration curve.

CONCLUSIONS: The LRT microbiome was altered in CAP patients. Indicator genera were shown to have the potential to serve as diagnosis biomarkers in the constructed predictive model. These results may provide further clues for the microbial pathogenesis, optimized diagnostics and new therapeutic targets of CAP.},
}

@article {pmid42880740,
year = {2026},
author = {Giono-Cerezo, S and López-Vidal, Y and Alcántar-Curiel, MD},
title = {Bacterial infections and their association with female infertility: diagnostic and therapeutic perspectives.},
journal = {Gaceta medica de Mexico},
volume = {162},
number = {1},
pages = {28-36},
doi = {10.24875/GMM.M26001104},
pmid = {42880740},
issn = {0016-3813},
mesh = {Humans ; Female ; *Infertility, Female/microbiology/etiology/therapy/diagnosis ; *Bacterial Infections/complications/diagnosis/therapy/microbiology/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Chlamydia Infections/complications/diagnosis ; Pregnancy ; },
abstract = {Infertility is a public health issue affecting millions of women of reproductive age worldwide. Bacterial infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, Mycoplasma hominis, and Ureaplasma urealyticum are among the most prevalent. They are associated with pelvic inflammatory disease, chronic endometritis, fallopian tube obstruction, impaired endometrial receptivity and implantation, and increased risk of ectopic pregnancy and pregnancy loss. Timely diagnosis using nucleic acid amplification testing represents the current standard, while advanced techniques, such as sequencing, enable the precise identification of pathogens and dysbiosis. The treatment of infections caused by these microorganisms involved the use of antibiotics, guided by the specific antimicrobial susceptibility pattern of each bacterium. Alternatives such as antioxidants, probiotics, or vaginal microbiota transplantation have been proposed for persistent infections. The clinical approach is interdisciplinary, incorporating imaging studies and inflammatory biomarkers. Understanding the pathogens and their interactions within the microbiome, along with the integration of reproductive medicine and clinical microbiology, provides valuable insights for managing and preserving female fertility.},
}

Humans
Female
*Infertility, Female/microbiology/etiology/therapy/diagnosis
*Bacterial Infections/complications/diagnosis/therapy/microbiology/drug therapy
Anti-Bacterial Agents/therapeutic use
Chlamydia Infections/complications/diagnosis
Pregnancy

@article {pmid42880793,
year = {2026},
author = {Stevens, NE and Botten, R and Geake, JB and Eden, GL and Lo, WK and Inauen, J and Solujic, J and Sawka, A and Yelland, LN and Reid, EW and Shaw, M and Zhu, X and Tam, TK and Jeon, H and Amenyogbe, N and Lynn, MA and Ryan, FJ and Feng, CG and Britton, WJ and Kollmann, TR and Barry, SE and Lynn, DJ},
title = {A randomised, placebo-controlled study to assess whether antibiotic-mediated disruption of the gut microbiota impairs BCG-induced specific and non-specific immunity in young, healthy adults: protocol for the Antibiotics and Vaccine Immune Responses Study (AVIRS).},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e126924},
doi = {10.1136/bmjopen-2026-126924},
pmid = {42880793},
issn = {2044-6055},
}

@article {pmid42880811,
year = {2026},
author = {Juanola, A and Moreta, MJ and Solé, C and Sánchez, J and Albillos, A and Martínez González, J and Poca Sans, M and Alvarado, E and Campos-Varela, I and Cespedes, C and Alonso, S and Bañares, R and Fortea, JI and Puente, Á and Llop, E and Fernández-Carrillo, C and Moya, A and Ruiz-Ruiz, S and Fernandez-Real, JM and Mayneris-Perxachs, J and Bonfill, E and Rivera, C and Pich, J and Piano, S and Solà, E and Torres, F and Iavarone, S and Pérez-Guasch, M and Casanova, NC and González-Suárez, B and Fabrellas, N and Graupera, I and Pose, E and Ginès, P},
title = {Randomised, double-blind, placebo-controlled trial of faecal microbiota transplantation in patients with decompensated cirrhosis: the Livergut protocol.},
journal = {BMJ open},
volume = {16},
number = {10},
pages = {e118486},
doi = {10.1136/bmjopen-2026-118486},
pmid = {42880811},
issn = {2044-6055},
}

@article {pmid42880833,
year = {2026},
author = {Moloney, GM and Clarke, G and Cryan, JF},
title = {Gut microbiota and epigenetic mechanisms in brain physiology and disorders.},
journal = {Handbook of clinical neurology},
volume = {219},
number = {},
pages = {147-167},
doi = {10.1016/B978-0-443-19043-8.00019-0},
pmid = {42880833},
issn = {0072-9752},
mesh = {Humans ; *Epigenesis, Genetic/physiology ; *Brain/physiology/metabolism ; Animals ; *Gastrointestinal Microbiome/physiology ; *Nervous System Diseases/genetics/microbiology ; *Brain Diseases/genetics ; },
abstract = {The interplay between gut microbiota and epigenetic mechanisms plays a crucial role in brain physiology and disorders, highlighting a novel area of research with significant implications for understanding and treating neurologic conditions. The gut microbiota, the diverse community of microorganisms in the digestive tract, influences brain function and health through the gut-brain axis, a complex communication network linking the gastrointestinal tract and the central nervous system. Epigenetic mechanisms, including DNA methylation, histone modification, and noncoding RNA activity, regulate gene expression without altering the DNA sequence, thus shaping neuronal development and plasticity. Recent studies have elucidated how gut microbiota can modulate these epigenetic processes, affecting neurotransmission, neuroinflammation, and the integrity of the blood-brain barrier. Disruptions in the gut microbiome are associated with various psychiatric disorders, such as autism spectrum disorder or depression, and with neurodegenerative diseases, potentially through epigenetic alterations that affect brain function. Understanding the molecular interactions between gut microbiota and epigenetic regulation offers promising avenues for therapeutic interventions, including dietary modifications, probiotics, and epigenetic drugs. This chapter underscores the significance of gut microbiota and epigenetic mechanisms in brain health and disease, suggesting that targeted manipulation of these factors could lead to novel treatments for neurologic disorders.},
}

Humans
*Epigenesis, Genetic/physiology
*Brain/physiology/metabolism
Animals
*Gastrointestinal Microbiome/physiology
*Nervous System Diseases/genetics/microbiology
*Brain Diseases/genetics

@article {pmid42881160,
year = {2026},
author = {Fernandes, N and Cai, M and Warren, FJ and Duncan, A and Harris, H and Serrano Contreras, JI and Sidorczuk, K and Bernal, A and Castillo, A and Petropoulou, K and Blunt, D and Perez-Moral, N and Garcia-Perez, I and Edwards, C and Hildebrand, F and Holmes, E and Wist, J and Frost, G},
title = {Effect of dietary chickpea structures on the small intestine metabolome and microbiome: a randomised crossover trial.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881160},
issn = {2041-1723},
support = {BB/X018857/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; },
mesh = {Humans ; Cross-Over Studies ; *Metabolome ; Glucagon-Like Peptide 1/metabolism ; Postprandial Period ; *Cicer/chemistry ; *Intestine, Small/metabolism/microbiology ; Peptide YY/metabolism ; Female ; Adult ; Gastric Inhibitory Polypeptide/metabolism ; *Gastrointestinal Microbiome/physiology ; Ileum/microbiology/metabolism ; *Diet ; Young Adult ; },
abstract = {The human gastrointestinal tract (GIT) is central to human physiology, yet our understanding of the metabolite, microbial, and hormonal spatiotemporal dynamics in humans is limited. How these environments respond to complex food structures and homeostatic mechanisms they generate is unknown in humans. In this randomised study, ten participants consumed chickpea-based meals with intact versus broken cellular structures, with sampling of oral, gastric, duodenal and ileal fluids. The primary outcome was the postprandial enteroendocrine hormone responses (GIP, GLP-1 and PYY); secondary outcomes were GIT metabolite profiles ([1]H NMR) and ileal microbiota (shotgun metagenomics). We observed that food structure markedly altered the spatiotemporal trajectories of metabolites and dominant microbe, driving distinct enteroendocrine hormone responses. Broken-cell meals produced early GIT glucose and maltose peaks associated with rapid GIP responses, whereas intact-cell meals elevated duodenal amino acids and ileal sugars, amino acids and formate, enhancing GLP-1 and PYY responses. Microbial profiles exhibited rapid spatial reorganisation, with evidence that oral bacterial strains transmitted to the ileum, where their abundance was associated with local metabolites and PYY responses. These findings identify food structure as a determinant of postprandial gastrointestinal metabolism and enteroendocrine responses and suggest an underappreciated route for oral bacteria to reach the ileum via the food bolus and impact metabolism. ISRCTN registration: ISRCTN18097249.},
}

Humans
Cross-Over Studies
*Metabolome
Glucagon-Like Peptide 1/metabolism
Postprandial Period
*Cicer/chemistry
*Intestine, Small/metabolism/microbiology
Peptide YY/metabolism
Female
Adult
Gastric Inhibitory Polypeptide/metabolism
*Gastrointestinal Microbiome/physiology
Ileum/microbiology/metabolism
*Diet
Young Adult

@article {pmid42881193,
year = {2026},
author = {Seymour, CO and Ecklu-Mensah, G and Lee, Y and Nicols, AR and Cheng, WA and Jumarang, JM and Marentes Ruiz, CJ and Navarro, J and Navarro, R and Rodriguez-Angeles, Y and Durand, D and Allard, SM and Taylor, ZW and De León, RG and Ochoa, TJ and Gilbert, JA and Pannaraj, PS},
title = {Klebsiella-dominant gut communities are associated with impeded oral rotavirus vaccine response in infants.},
journal = {Nature communications},
volume = {17},
number = {1},
pages = {},
pmid = {42881193},
issn = {2041-1723},
mesh = {Humans ; *Rotavirus Vaccines/immunology/administration & dosage ; *Rotavirus Infections/prevention & control/immunology/virology/microbiology ; Infant ; Feces/microbiology/chemistry ; Rotavirus/immunology ; *Klebsiella/isolation & purification/immunology ; *Gastrointestinal Microbiome/immunology ; Gastroenteritis/prevention & control/virology/microbiology/immunology ; Administration, Oral ; Virus Shedding ; Female ; Male ; Peru ; Leukocyte L1 Antigen Complex ; Immunogenicity, Vaccine ; },
abstract = {Rotavirus gastroenteritis is the leading cause of infant diarrheal death worldwide. Oral rotavirus vaccine (RVV) prevents illness and death, but efficacy differs between high- and low-income countries and the etiologies are unclear. Here, we describe the relationship between colonization of the infant gut by commensal bacteria, inflammation, and vaccine response across a cohort of infants from Panama, Peru, and the U.S. Vaccine immunogenicity was related to community composition in the first month of life and inverse to increased relative abundance of Klebsiella. Clustering communities into gut types revealed that microbiome configurations with elevated Klebsiella or Escherichia in the first month of life were negatively associated with both seroconversion and rotavirus shedding after vaccination, suggesting potential inhibition of vaccine function or host response. Infants without RVV strain shedding displayed elevated fecal calprotectin in the first month. These results implicate microbiome-augmented infant gut inflammation as a potential impediment to RVV response.},
}

Humans
*Rotavirus Vaccines/immunology/administration & dosage
*Rotavirus Infections/prevention & control/immunology/virology/microbiology
Infant
Feces/microbiology/chemistry
Rotavirus/immunology
*Klebsiella/isolation & purification/immunology
*Gastrointestinal Microbiome/immunology
Gastroenteritis/prevention & control/virology/microbiology/immunology
Administration, Oral
Virus Shedding
Female
Male
Peru
Leukocyte L1 Antigen Complex
Immunogenicity, Vaccine

@article {pmid42881207,
year = {2026},
author = {Haskell, J},
title = {Engineering gut microbiome states overcomes hepatic accumulation of nanomedicines.},
journal = {Nature biomedical engineering},
volume = {10},
number = {10},
pages = {1988},
doi = {10.1038/s41551-026-01811-7},
pmid = {42881207},
issn = {2157-846X},
}

@article {pmid42881491,
year = {2026},
author = {Zehra, H and Kuchma, N and Lin, AW and Morris, G and Solano, O and Lopez, S and Kabage, AJ and Vaughn, BP and Weingarden, A and Fischer, M and Khoruts, A and Teigen, L},
title = {The Trajectory of Gastrointestinal Symptom Experience Following Fecal Microbiota Transplant for Recurrent Clostridioides Difficile Infection.},
journal = {Journal of clinical gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1097/MCG.0000000000002424},
pmid = {42881491},
issn = {1539-2031},
abstract = {INTRODUCTION: Recurrent Clostridioides difficile infection (rCDI) increases the risk of persistent gastrointestinal symptoms after treatment. Although fecal microbiota transplantation (FMT) effectively prevents CDI recurrence after antibiotics, the trajectory of gastrointestinal symptom severity remains poorly characterized.

METHODS: We tracked gastrointestinal symptom severity in a prospective, multicenter cohort study of adults with rCDI after treatment with standardized FMT products. Patients who experienced a CDI recurrence during the follow-up period were excluded. The IBS Symptom Severity Scale (IBS-SSS) was used as a measure of symptom severity, not as a diagnostic tool. Patients completed the IBS-SSS at the time of FMT, 1-week, 1-month, and 3-months post-FMT. The primary outcome was the change in IBS-SSS score after treatment. Subgroup analyses were conducted among patients with baseline IBS-SSS ≥175 (moderate/severe symptom severity) and <175 (none/mild symptom severity). Linear mixed-effects models were used to evaluate longitudinal changes and identify clinical predictors of IBS-SSS scores.

RESULTS: Among 107 patients included, median IBS-SSS scores decreased from 170 (range: 0 to 440) at baseline to 76 (range: 0 to 390) at week 1 and 54 (0 to 445) at month 3 (P<0.001). In those with baseline IBS-SSS ≥175 (n=51), 64% had none or mild symptom severity at month 3. In those with baseline IBS-SSS <175 (n=53), symptom severity was observed to remain as none or mild at month 3 in all but one patient.

CONCLUSION: FMT administered for prevention of rCDI was followed by a rapid (1 wk) and sustained (3 mo) reduction in gastrointestinal symptom scores in patients who did not develop CDI recurrence. These data help characterize the expected early post-FMT symptom trajectory, providing foundational evidence to better inform patient expectations and future interventions for persistent symptoms.},
}

@article {pmid42881525,
year = {2026},
author = {Chen, C and Zhang, H and Cheng, T and Zhou, F and Chen, X and Fang, M and Qi, P},
title = {Oral microbiome and inflammatory bowel disease: A scoping review.},
journal = {American journal of dentistry},
volume = {39},
number = {5},
pages = {253-258},
pmid = {42881525},
issn = {0894-8275},
mesh = {Humans ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; *Mouth/microbiology ; Dysbiosis/microbiology ; Periodontitis/microbiology ; Saliva/microbiology ; },
abstract = {PURPOSE: To examine the association between the oral microbiome and IBD in terms of microbiota diversity, composition, function, and diagnostic potential through a scoping review of the existing literature.

METHODS: This scoping review was structured following the PRISMA-ScR guidelines. Literature searches were conducted in PubMed, Embase, and the Cochrane Library, with the time frame restricted from database inception to November 17, 2025.

RESULTS: This review included 31 studies, among which seven topics for patients with periodontitis and IBD-related periodontitis, three studies assessed single bacterial species, and the remaining 21 articles explored the diversity and phylum-level taxonomic shifts of oral microbiota in IBD patients, functional and metabolic pathway alterations associated with oral dysbiosis, as well as the diagnostic potential and biomarkers derived from oral microbial profiles.

CLINICAL SIGNIFICANCE: The oral microbiota of IBD patients exhibits characteristic dysbiosis, manifested by the enrichment of pathogenic taxa, depletion of anti-inflammatory species, and metabolic dysfunction, which are closely associated with gut microbial alterations and systemic inflammatory status. The salivary microbiome demonstrates significant diagnostic potential for IBD.},
}

Humans
*Inflammatory Bowel Diseases/microbiology
*Microbiota
*Mouth/microbiology
Dysbiosis/microbiology
Periodontitis/microbiology
Saliva/microbiology

@article {pmid42881712,
year = {2026},
author = {Ionaș, TH and Ionaș, M and Chicea, R and Stănilă, A and Boța, G},
title = {Self-Reported Prebiotics and Probiotics Recognition and Recommendation Practices Among Dentists in Sibiu County, Romania: A Cross-Sectional Questionnaire Survey.},
journal = {Healthcare (Basel, Switzerland)},
volume = {14},
number = {19},
pages = {},
doi = {10.3390/healthcare14193274},
pmid = {42881712},
issn = {2227-9032},
abstract = {Background/Objectives: Probiotics and prebiotics are being investigated as adjuncts for the management of oral dysbiosis, but little is known about how dentists understand and recommend them. We describe self-reported recognition of oral microbiome concepts, identification of the definitions of prebiotics and probiotics, and recommendation practices among dentists in Sibiu County, Romania. Methods: A cross-sectional online questionnaire survey (comprising eight closed items; delivered using Google Forms) was distributed through the county professional association WhatsApp messaging channel and to personal contacts between 20 February 2026 and 9 March 2026. Of a target of 630 dentists, 107 completed the questionnaire (response rate: 17.0%), forming a voluntary local sample. Three pre-specified hypotheses (definition accuracy × recommendation; general recommendation × adjunct recommended during antibiotic therapy; and years of experience × definition accuracy and recommendation) were tested with exact tests, odds ratios (ORs), and 95% confidence intervals (CIs) with Holm adjustment; other item associations were exploratory and adjusted within families. Results: A microbial role was recognized for periodontal disease by 98.1% of respondents, for dental caries by 92.5%, for focal infection by 73.8%, and for bone infection of dental origin by 64.5%. Diet, antibiotics, oral hygiene, and smoking were recognized as microbial influencing factors by 78-84%, probiotics by 58.9%, and prebiotics by 52.3%. Definitions of the adjuncts were correctly identified by 83.2% (prebiotics) and 80.4% (probiotics). Prebiotics were recommended by 50.5% and probiotics by 86.0% of respondents. Correct definitions were not associated with recommendation (prebiotics: OR 1.76, 95% CI 0.62-4.95; probiotics: OR 1.60, 95% CI 0.46-5.65). During antibiotic therapy, dentists who recommended prebiotics were more likely to select a prebiotic-probiotic combination than those who did not (57.4% versus 3.8%; exact p < 0.001). No outcome differed by years of experience. Conclusions: In this self-selected sample, biotics were recognized as microbiome-influencing factors less often than classical factors, and knowing the definitions was not associated with recommending the products. The reasons behind recommendation habits were not measured and require dedicated study.},
}

@article {pmid42882080,
year = {2026},
author = {Caruso, F and Vigilante, L and Borrelli, D and Gallo, A and Strina, I and Di Spiezio Sardo, A and Fantuz, MR and Savarese, G},
title = {Recurrent Implantation Failure and the Gut-Endometrium Axis: A Pilot Study on Microbiota Crosstalk.},
journal = {Journal of clinical medicine},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/jcm15197620},
pmid = {42882080},
issn = {2077-0383},
abstract = {Objective: We aim to assess gut and endometrial microbiota simultaneously in women with unexplained recurrent implantation failure (RIF) and explore the hypothesis of a gut-endometrium microbial axis. Study design: This monocentric observational pilot study included women aged 38 years or younger with a history of RIF. Paired fecal and endometrial samples were collected on the same day and analyzed by 16S rRNA gene sequencing. Relative abundances of major phyla and alpha-diversity indices were compared between compartments. Results: Twenty-one women were included. Chronic endometritis was documented through hysteroscopy in all cases. Gut dysbiosis was observed in 20/21 patients (95.2%), whereas endometrial dysbiosis was found in 16/21 (76.2%); crude agreement between compartments was 71.4% (Gwet's AC1 0.62, 95% CI 0.25-0.90). The intestinal microbiota was dominated by Bacteroidetes (52.8% ± 14.9%) and Firmicutes (33.3% ± 11.0%), whereas the endometrial microbiota was enriched in Firmicutes (64.5% ± 33.5%) and Proteobacteria (30.9% ± 32.3%). Bacteroidetes were significantly more abundant in fecal than endometrial samples (p < 0.001), while Firmicutes were significantly enriched in the endometrium (p = 0.001). All alpha-diversity indices were significantly higher in feces, indicating greater microbial richness and complexity in the gut. Conclusions: In this pilot cohort of women with unexplained RIF, gut and endometrial dysbiosis frequently co-occurred. These findings support a potential gut-endometrium microbial axis and highlight the possible interplay between gut and endometrial microbiota in recurrent implantation failure. Further studies are warranted to better elucidate the clinical and biological implications of this relationship.},
}

@article {pmid42882437,
year = {2026},
author = {Nitsotolis, TN and Assimakopoulos, SF and Mastoridou, E and Kolios, NG and Biros, D and Oikonomidi, ED and Lagadinou, M and Papalexandrou, A and Milionis, H and Christaki, E and Kalambokis, G},
title = {Cellular Crosstalk at the Gut-Liver Interface in Liver Cirrhosis: Epithelial Barrier Failure, Bacterial Translocation and Immune Activation as a Bidirectional Network.},
journal = {Cells},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/cells15191739},
pmid = {42882437},
issn = {2073-4409},
mesh = {Humans ; *Bacterial Translocation ; *Liver Cirrhosis/immunology/microbiology/pathology ; Animals ; *Liver/pathology/immunology/microbiology ; Intestinal Barrier Function ; *Intestinal Mucosa/pathology ; },
abstract = {The gut-liver axis is central to the systemic complications of liver cirrhosis, but it is usually described as a linear cascade in which barrier failure releases microbial products that activate a downstream immune response. This review proposes instead a four-compartment framework, in which the epithelial/barrier, innate immune, adaptive effector, and stromal-endothelial compartments-the last including the gut-vascular barrier-are treated as reciprocally interacting nodes, and pathological bacterial translocation is treated as both an input to and an output of the network rather than as its endpoint. Applying this framework across the stages of cirrhosis, we examine how tight-junction disassembly, mucus-layer thinning, Paneth-cell dysfunction and reduced secretory IgA, together with dysbiosis and small-intestinal bacterial overgrowth, permit translocation; how translocated bacteria and pathogen-associated molecular patterns activate all four compartments; and how the resulting cytokine circuits further degrade the barrier, generating feed-forward loops that underlie cirrhosis-associated immune dysfunction and chronic systemic inflammation. We relate these circuits to spontaneous bacterial peritonitis, hepatic encephalopathy, aggravated portal hypertension, and acute-on-chronic liver failure, distinguishing throughout between mechanisms demonstrated in humans and those inferred from animal or in vitro models. We identified evidence through structured searches of PubMed/MEDLINE, Embase, and Web of Science, and report it according to the SANRA checklist. Framed as a network, biomarkers become compartment-specific reporters, and barrier-, microbiome-, and immune-directed therapies become interventions at defined nodes and edges-a view that clarifies both their rationale and the current limits of the evidence.},
}

Humans
*Bacterial Translocation
*Liver Cirrhosis/immunology/microbiology/pathology
Animals
*Liver/pathology/immunology/microbiology
Intestinal Barrier Function
*Intestinal Mucosa/pathology

@article {pmid42882498,
year = {2026},
author = {Siemińska, I},
title = {The Gut Microbiota-Immunity Axis in Colorectal Cancer: Implications for Immunotherapy and Clinical Translation.},
journal = {Cells},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/cells15191800},
pmid = {42882498},
issn = {2073-4409},
mesh = {Humans ; *Colorectal Neoplasms/immunology/therapy/microbiology ; *Immunotherapy/methods ; *Gastrointestinal Microbiome/immunology ; *Translational Research, Biomedical ; Animals ; *Immunity ; },
abstract = {Colorectal cancer (CRC) arises within a complex microbial ecosystem that may influence carcinogenesis, tumor immunity, and therapeutic response. This is particularly relevant in metastatic disease, where most tumors are microsatellite-stable/mismatch repair-proficient (MSS/pMMR) and derive little meaningful benefit from immune checkpoint inhibitor (ICI) monotherapy. Specific pathobionts, including Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, have been implicated in genotoxic, inflammatory, and checkpoint-related mechanisms that may contribute to tumor progression and immune evasion, whereas selected commensals and microbiota-derived metabolites may support antitumor immunity in a context-dependent manner. This review integrates translational evidence linking microbial taxa and functions, metabolites, neutrophil biology, bacterial extracellular vesicles, and T-cell dysfunction with CRC progression and immunotherapy response. This review critically examines emerging microbiome-directed strategies, including fecal microbiota transplantation, next-generation probiotics, defined bacterial consortia, dietary and perioperative interventions, postbiotics, and bacteriophage-based approaches, as potential means of modifying immune resistance in MSS/pMMR CRC. Although early clinical signals from microbiota-modulating combinations are encouraging, the available evidence remains limited by small cohorts, heterogeneous interventions, and the absence of randomized CRC-specific studies. Microbiome-based biomarkers and therapeutics therefore remain investigational, and standardized sampling, prospective validation, and carefully designed trials will be required before microbiome modulation enters routine CRC care.},
}

Humans
*Colorectal Neoplasms/immunology/therapy/microbiology
*Immunotherapy/methods
*Gastrointestinal Microbiome/immunology
*Translational Research, Biomedical
Animals
*Immunity

@article {pmid42882521,
year = {2026},
author = {Pînzariu, AC and Șerban, IL and Soroceanu, RP and Vlăsceanu, VI and Maxim, M and Miler, AA and Leonte, SM and Atodiresei, C and Moscalu, M and Manole, LM and Trandafir, LM and Șerban, DN and Timofte, DV},
title = {GDF-15/GFRAL Axis Dynamics and Vulnerability Windows in Bariatric Surgery: Pathophysiological, Microbiomic, and Pharmacological Perspectives.},
journal = {Cells},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/cells15191823},
pmid = {42882521},
issn = {2073-4409},
mesh = {Humans ; *Bariatric Surgery ; Animals ; *Growth Differentiation Factor 15/metabolism ; *Glial Cell Line-Derived Neurotrophic Factor Receptors/metabolism ; Gastrointestinal Microbiome ; Signal Transduction ; Obesity/surgery/metabolism ; },
abstract = {Bariatric surgery (BS) and new pharmacological treatments cause significant neurometabolic changes. However, the pathways linking peripheral stress to central metabolic control remain poorly understood. This review highlights the GDF-15/GFRAL/RET complex as a key integrator of multiorgan-to-brain stress signals that shape systemic metabolic adaptation after surgical and pharmacological interventions. Based on a structured search across PubMed, Embase, Scopus, Google Scholar, and Web of Science covering 2020-2026 alongside foundational studies, we integrated translational evidence from peer-reviewed human trials and mechanistic animal models to map the GDF-15/GFRAL/RET axis across bariatric and incretin domains. We examined the neurobiology of the GDF-15/GFRAL axis to clarify variability in metabolic and behavioral outcomes after BS. This axis links metabolic stress signals from the gut, liver, and adipose tissue to the hindbrain and hypothalamic regulation of energy balance. Changes in the gut microbiome and SCFA-FFAR2/FFAR3 signaling after surgery interact with GDF-15 and incretin pathways. Future studies should critically compare BS with synergistic or alternative non-invasive neurometabolic approaches such as incretin mimetics, exogenous GDF-15 therapies, and high-protein diets.},
}

Humans
*Bariatric Surgery
Animals
*Growth Differentiation Factor 15/metabolism
*Glial Cell Line-Derived Neurotrophic Factor Receptors/metabolism
Gastrointestinal Microbiome
Signal Transduction
Obesity/surgery/metabolism

@article {pmid42882861,
year = {2026},
author = {Machado, MV},
title = {Prediction of Response to Immunotherapy in Hepatocellular Carcinoma: Where Do We Stand?.},
journal = {Cancers},
volume = {18},
number = {19},
pages = {},
doi = {10.3390/cancers18193167},
pmid = {42882861},
issn = {2072-6694},
abstract = {Worldwide, liver cancer is the seventh most common cancer and the third leading cause of cancer-related mortality, reflecting its dismal prognosis, with only approximately 20% of patients alive 5 years after diagnosis. At least 50% of patients ultimately require systemic treatment. In 2020, the systemic treatment landscape changed dramatically with the introduction of immune checkpoint inhibitor (ICI)-based therapies, which have demonstrated improved overall survival and longer preservation of quality of life compared with tyrosine kinase inhibitor (TKI)-based approaches. However, fewer than one third of patients achieve objective response, 10-25% experience severe immune-related adverse events, and ICI-based treatments represent a substantial economic burden for health systems. Importantly, robust and clinically validated predictive biomarkers of response to ICI remain an unmet need. This review summarizes current efforts to identify predictive biomarkers of ICI response in hepatocellular carcinoma (HCC), integrating clinical, pathological, molecular, microbiome, and imaging approaches, and discusses how these developments may shape the future of treatment selection.},
}

@article {pmid42883021,
year = {2026},
author = {Bao, J and Li, H and Jiang, K and Xu, J and Wu, Y and Ji, W and Li, S and Qi, B and Niu, H},
title = {Comparative Study on Growth Performance and Rumen Digestive Metabolism Between Cull Beef Cows and Fattening Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193052},
pmid = {42883021},
issn = {2076-2615},
support = {(32460813)//National Natural Science Foundation of China/ ; (2025YFDZ0123, 2025ZY0111, YZ2023010, TL20205TW004)//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; (GXKY26Z082).//Inner Mongolia University for Nationalities/ ; },
abstract = {Culled beef cows may retain practical value for fattening after reproductive use, but the rumen and host physiological characteristics associated with this response remain incompletely characterized. This study compared culled beef cows (CBC; n = 9) with fattening bulls (CON; n = 9) using 18 healthy Simmental crossbred cattle fed the same experimental total mixed ration (TMR) under identical feedlot conditions. Growth performance, body condition score (BCS), apparent nutrient digestibility, economic outcomes, blood indices, rumen fermentation, ruminal enzyme activities, rumen metagenomes, and plasma untargeted metabolomes were assessed. Compared with CON, CBC had higher final body weight, average daily gain, feed intake, and apparent digestibility of dry matter, crude protein, and neutral detergent fiber, whereas the feed-to-gain ratio did not differ significantly between groups (p = 0.692). BCS increased significantly from day 0 to day 60 within both cattle categories. Because different, non-cross-calibrated BCS reference frameworks were used, no between-group comparison of BCS was made. Economic analysis indicated that the value attributable to actual live-weight gain was similar between groups when within-category prices were held constant, whereas the relative economic outcome varied with feed costs and changes in live-cattle market prices. CBC also showed more propionate-oriented fermentation, greater fibrolytic enzyme activities, distinct carbohydrate-active enzyme profiles, higher insulin and leptin, and lower non-esterified fatty acids and β-hydroxybutyrate. Because lean and fat mass were not directly measured, the tissue basis of the greater weight gain remains unresolved. Overall, CBC exhibited a stronger fattening response accompanied by coordinated differences in rumen function and host metabolic profiles.},
}

@article {pmid42883069,
year = {2026},
author = {Kostyunina, O and Traspov, A and Ermilov, A and Bakoev, F and Nemkovskiy, G and Kusnetzov, A and Belyakov, V},
title = {Untargeted Metabolomic Profiling of Spermatozoa and Seminal Plasma Identifies Candidate Metabolic Indicators of Semen Quality in Holstein Bulls.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193098},
pmid = {42883069},
issn = {2076-2615},
support = {24-16-00198//Russian Science Foundation/ ; },
abstract = {This exploratory study applied untargeted LC-MS/MS metabolomic profiling to investigate metabolic differences between Holstein bulls with high-quality (HQ) and low-quality (LQ) semen in both spermatozoa and seminal plasma. Bulls were classified based on long-term routine semen quality records and ejaculate rejection rates, providing a stable and biologically meaningful grouping. A total of 249 unique metabolites were annotated across both biological matrices. Differential analysis identified 46 LC-MS features corresponding to 44 unique metabolites in spermatozoa and 11 LC-MS features corresponding to 9 unique metabolites in seminal plasma that met the predefined multi-criteria selection thresholds (FDR < 0.05, |log2FC| > 1, VIP > 1, and AUC ≥ 0.80 or ≤0.20). The HQ group was characterized by higher levels of metabolites involved in amino acid and energy metabolism, including glutamine, glutamate, aspartate, succinate, ornithine, citrulline, and arginine. Conversely, the LQ group showed increased abundance of metabolites potentially related to altered redox homeostasis and compounds potentially originating from dietary or microbial sources. As this is an exploratory study, mechanistic interpretations regarding oxidative stress, microbiome-derived metabolites, and actual fertility should be considered strictly hypothesis-generating. The annotated metabolites represent candidate indicators associated with semen quality parameters rather than validated biomarkers. Their relationship with actual field fertility and their underlying biological mechanisms require confirmation in larger, independent populations with direct functional assays and field fertility records.},
}

@article {pmid42883122,
year = {2026},
author = {Baka, E and Kovács-Weber, M and Ábrahám, R and Pap, TI and Táncsics, A and Szabó, G and Heincinger, M and Szabó, S and Dolányi, Á and Berta, AI and Kovács, B and Szabó, RT},
title = {A Paired Ileum-Caecum Study of the Goose Gut Microbiome in Response to Fattening Protocol and Postbiotic Supplementation.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {19},
pages = {},
doi = {10.3390/ani16193153},
pmid = {42883122},
issn = {2076-2615},
support = {//Hungarian University of Agriculture and Life Sciences/ ; },
abstract = {The gut microbiota plays a central role in poultry health and production performance, yet its response to intensive fattening protocols and postbiotic supplementation in geese remains poorly characterized. This study used 16S rRNA gene amplicon sequencing to profile ileal and caecal microbial communities from geese raised under two fattening protocols, with or without postbiotic supplementation, and assessed the effect of 24 h post-mortem chilling on apparent community composition. Fattening protocol was associated with the largest differences in gut microbial structure, producing significant shifts in beta diversity in both the ileum and the caecum (although protocol, age at slaughter, and duration of postbiotic exposure co-varied between cohorts and cannot be fully disentangled), accompanied by extensive taxon-level differences identified by LEfSe. Postbiotic supplementation did not significantly alter overall community structure under force-feeding conditions but produced a taxon-specific, trend-level shift in the caecum under restricted feeding, suggesting that its effect depends on the continuity of supplementation relative to slaughter. Alpha diversity did not differ significantly in the ileum, but caecal richness differed significantly between the G2 and G5 postbiotic-supplemented groups (Conover-Iman test, adjusted p < 0.05). The warm- and chilled-dissection groups differed in ileal but not caecal community composition (individual-animal variation cannot be separated from the effect of chilling in this comparison, as the two groups consisted of different birds), indicating that dissection timing is an important methodological variable in goose microbiome research. These findings highlight cohort- and protocol-related differences as key correlates of gut microbial composition in geese and provide a framework for optimizing postbiotic supplementation strategies and sampling standardization in waterfowl production.},
}

@article {pmid42883403,
year = {2026},
author = {Khan, ZA and Chowdhury, Z and Modi, R and Sumsuzzman, DM and Ju, LS and Labala, RK and Gravenstein, N and Martynyuk, AE},
title = {Gut Microbiome Disruption in Traumatic Brain Injury and Therapeutic Potential of Probiotics: A Systematic Review and Meta-Analysis.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191730},
pmid = {42883403},
issn = {2079-7737},
support = {1R01HD107722-05/NH/NIH HHS/United States ; 5R56HD102898-02/NH/NIH HHS/United States ; //I. Heerman Anesthesia Foundation/ ; },
abstract = {BACKGROUND: Traumatic brain injury (TBI) is increasingly recognized as a systemic disorder that may involve alterations in the brain-gut-microbiome (BGM) axis, a bidirectional network linking the brain, immune system, and gut microbiota. While animal studies suggest that disruption and restoration of the BGM axis influence TBI-related changes and recovery, respectively, human evidence remains fragmented.

METHODS: MEDLINE, Embase, Scopus, and Web of Science were searched through 2025; Global Health was additionally searched for Aim 2. This study had two aims: (1) to assess gut microbiome changes following TBI and (2) to evaluate the effects of probiotic supplementation in TBI patients. Data were synthesized using random-effects meta-analyses, and risk of bias was assessed using the Newcastle-Ottawa and Cochrane tools.

RESULTS: Five studies (Aim 1) and fifteen studies (Aim 2) met the inclusion criteria. TBI was associated with shifts in microbial composition, including reduced abundance of Prevotella (p < 0.001), and Parabacteroides merdae (p = 0.038), whereas overall alpha diversity did not differ significantly. Probiotic supplementation improved neurological outcomes [Glasgow Coma Scale (GCS): MD = 2.25, 95% CI 1.34-3.16, p < 0.001] and functional outcomes [Glasgow Outcome Scale (GOS): MD = 1.40, 95% CI 1.12-1.69, p < 0.001], and reduced inflammatory markers, including TNF-α (p = 0.006), IL-6 (p < 0.001), procalcitonin (p < 0.001), and D-lactic acid levels (p < 0.001). High heterogeneity was observed across several outcomes, with the GOS showing moderate heterogeneity. Neurocognitive outcomes were evaluated qualitatively and were not pooled in a meta-analysis because of limited available data.

CONCLUSIONS: The findings of this analysis suggest that TBI is associated with alterations in the gut microbiome and that microbiota-targeted therapies involving probiotics may improve inflammatory, gut-barrier, neurological, and functional outcomes. Although substantial heterogeneity was observed across several outcomes, particularly the GCS, the available evidence supports further investigation of microbiome-directed interventions as adjunctive strategies for TBI management. Standardized multicenter trials are warranted.

PROSPERO: CRD420251135998.},
}

@article {pmid42883405,
year = {2026},
author = {Hammami, I and Abdelaal, M and Ababutain, IM and Alsanie, SI and Al Hawas, GH and Alghamdi, AI and Alqazlan, NM and Alghamdi, RA and Alsubaie, FM and Alnabbat, JY},
title = {Integrated Phytoremediation and Microbial Mitigation Strategies for Sustainable Restoration of Toxic Metal-Contaminated Soils.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191732},
pmid = {42883405},
issn = {2079-7737},
abstract = {Toxic metal contamination of soil remains a critical global challenge due to the persistence, bioaccumulation, and irreversible toxicity of these metals. Cadmium (Cd), lead (Pb), mercury (Hg), arsenic (As), chromium (Cr) and nickel (Ni) are the most common toxic metals that threaten food security, ecosystem stability, and human health. While conventional physicochemical remediation technologies provide rapid pollutant removal, they are constrained by high economic costs, secondary pollution risks, and long-term soil degradation. Biological approaches, particularly phytoremediation and microbial mitigation, offer environmentally compatible alternatives; however, their field-scale performance is often limited by low biomass production, restricted metal bioavailability, microbial instability, and heterogeneous soil conditions. This review critically synthesizes recent advances that move beyond standalone biological strategies toward integrated, multi-scale remediation frameworks. We evaluate the mechanistic basis and performance of nano-assisted phytoremediation, biochar-mediated stabilization, omics-guided plant-microbe optimization, and clustered regularly interspaced short palindromic repeats/CRISPR-associated protein systems (CRISPR/Cas) for enhancing metal transport, chelator biosynthesis, antioxidant defense, and microbial detoxification pathways. Emerging evidence indicates that nano-enabled amendments and biochar composites can reduce bioavailable Cd fractions by up to 75%, while omics-driven microbial consortia and targeted genome editing improve tolerance and accumulation efficiency in key crops such as rice and sorghum. Importantly, we assess translational barriers including nanoparticle ecotoxicity, off-target genome effects, regulatory constraints, biomass disposal, and life-cycle sustainability that currently limit large-scale deployment. By integrating mechanistic insights with field validation data, risk assessment considerations, and technology readiness evaluation, this review proposes a conceptual roadmap for scalable, eco-efficient soil restoration. The convergence of nanotechnology, systems biology, microbiome engineering, and precision genome editing represents a transformative pathway for next-generation remediation strategies capable of restoring contaminated soil while safeguarding environmental and public health.},
}

@article {pmid42883411,
year = {2026},
author = {Florez, JZ and Varela-Prieto, L and Zárate, A and Caselles-Osorio, A and Llanos-Lizcano, A and Bruna, P},
title = {Root Microbiome Assembly Underpins the Ecological Role of Emergent Macrophytes in a Pilot-Scale Constructed Wetland.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191739},
pmid = {42883411},
issn = {2079-7737},
support = {11250731//National Agency for Research and Development/ ; 3220504//National Agency for Research and Development/ ; 2023-21230832//National Agency for Research and Development/ ; },
abstract = {Constructed wetlands (CWs) depend on plant-microbe associations for pollutant transformation, yet the processes linking macrophyte identity to rhizosphere microbiome assembly remain insufficiently resolved. We compared bacterial communities associated with C. articulatus (Ca) and T. geniculata (Tg) roots with an unplanted treatment (Up) in pilot-scale CWs on the Colombian Caribbean coast. Bacterial communities were characterized by 16S rRNA gene amplicon sequencing. Co-occurrence networks, taxon-environment correlations, and the phylogenetic bin-based null model iCAMP were used to assess community structure, potential associations and assembly mechanisms. CaS supported significantly greater bacterial diversity than TgS and Up, while each macrophyte recruited a distinct community. A shared core microbiome dominated by Rhodocyclaceae, Sphingomonadaceae, Chitinophagaceae, Pirellulaceae, and Xanthomonadaceae comprised taxa with putative roles in nutrient and organic matter transformations. Several bacterial families were significantly associated with PO4[3-], NH4[+], and dissolved oxygen. Assembly was predominantly stochastic, with dispersal limitation (45.2%) and ecological drift (33.2%) exceeding deterministic selection (16.5%). Nevertheless, planted treatments displayed higher network modularity and connectivity and inferred functional redundancy than Up, consistent with niche differentiation. These findings suggest that species-specific macrophyte configurations are associated with differences in root-associated microbial community composition, while assembly and network analyses provide exploratory insights into community organization. The limited replication precludes causal attribution to plant identity or conclusions regarding treatment performance. Future studies integrating controlled planting densities, increased replication, meta-omics, and root exudate characterization are needed to clarify plant-microbiome relationships and evaluate their potential relevance to constructed wetland functioning.},
}

@article {pmid42883451,
year = {2026},
author = {Liu, L and Spaink, HP},
title = {TLR Signaling Beyond Immunity: Emerging Roles in Cell Migration, Metabolism, Development, and Host-Microbiome Crosstalk.},
journal = {Biology},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/biology15191778},
pmid = {42883451},
issn = {2079-7737},
abstract = {Recent findings support a broader view of TLR signaling as an integrative signaling hub that links immunity with cell migration, metabolism, development, and host-microbiome crosstalk. In cell migration, TLRs exert context-dependent effects through chemokine receptor regulation, adhesion and cytoskeletal modulation, and indirect cytokine-mediated signaling. In metabolism, TLRs orchestrate insulin resistance, obesity, and glucose homeostasis in a receptor- and tissue-specific manner. In tissue injury and development, TLR signaling exerts dual roles; it is detrimental in ischemia-reperfusion injury, but beneficial in vascular remodeling and neurogenesis. We then examine the bidirectional interplay between TLRs and the gut microbiome, where TLRs shape microbial community structure and intestinal immune homeostasis. Finally, we survey the therapeutic landscape of TLR modulators, highlighting that while TLR agonists are predominantly explored in oncology, TLR antagonists show promise in autoimmune diseases such as inflammatory bowel disease. Special attention is given to insights from organoid, rodent and zebrafish models, which have provided powerful in vitro and in vivo evidence for multiple roles of TLR signaling under both physiological and pathological conditions. A deeper understanding of these non-canonical functions will be essential for developing next-generation therapeutic strategies that selectively modulate TLR signaling in infectious, inflammatory, metabolic, and microbiome-associated diseases.},
}

@article {pmid42883591,
year = {2026},
author = {Jiang, X and Xu, H and Zhou, H and Xie, M and Xiong, T and Liu, Z},
title = {Exploring Dynamic Changes in Microbial Succession and Flavor-Active Metabolites During Pickled and Dried Mustard Fermentation of Traditional Fermented Vegetables.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/foods15193486},
pmid = {42883591},
issn = {2304-8158},
support = {32260576//National Natural Science Foundation of China/ ; 20232BBF60024//Jiangxi Provincial KeyR&D Program/ ; 202401AS070025//Yunnan Provincial Basic Research Program in 2024/ ; },
abstract = {Pickled and dried mustard (PDM) is a traditional dish of the Hakka people that is well-known in many parts of the world. However, past scientific studies on PDM provide little information on the relationship between the microbiome composition of the PDM fermentation process and flavor formation, which restricts the industrialization and improved quality control of PDM. Therefore, this study investigated the microbiome composition, flavor metabolites, physicochemical properties, and the relationships among them in PDM from Shaoxing. During fermentation, the main aromas of PDM are similar to pine and orange oils, with a strong fat aroma, and are mainly contributed by dodecanal in the early and middle stages of fermentation. As the fermentation progressed, the phenolic and aldehyde contents increased markedly; the major aldehydes in PDM were dodecanal, nonanal, and phenylacetaldehyde. The microbial succession during PDM fermentation was a gradual transition from Weissella sp. and Basidiomycota to Latilactobacillus, Lactiplantibacillus, and Ascomycota. We identified candidate core microorganisms potentially related to characteristic flavor development in PDM: Debaryomyces sp., Weissella cibaria, Lactiplantibacillus pentosus, Weissella sp. NBRC 107272, Latilactobacillus sakei, Cryptococcus sp., Filobasidium magnum, Cystofilobasidium macerans, Weissella hellenica, Levilactobacillus brevis, and Weissella sp. NBRC 107245. The findings of this study will be an important guide to optimizing the production process and quality of PDM.},
}

@article {pmid42883631,
year = {2026},
author = {Eltanty, MM and Shim, JH and Türkez, H and Bae, SJ and Bae, J and Abd El-Aty, AM},
title = {From Food Additives and Contaminants to the Human Exposome: A Precision Toxicology Framework for Next-Generation Food Safety.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {19},
pages = {},
doi = {10.3390/foods15193525},
pmid = {42883631},
issn = {2304-8158},
support = {2026-ANCHOR-15-110//Ministry of Education/ ; RS-2026-25477916//National Research Foundation of Korea/ ; },
abstract = {Human exposure to foodborne xenobiotics, including environmental contaminants that enter the food chain, is no longer adequately represented by isolated chemicals. Individuals encounter complex and dynamic mixtures of food additives, pesticide residues, veterinary drugs, mycotoxins, processing contaminants, packaging migrants, environmental pollutants, and other dietary chemicals that interact with genetics, metabolism, the gut microbiome, nutritional status, and lifestyle throughout life. The dietary exposome therefore represents a critical interface linking food contaminants, internal chemical exposure, molecular perturbation, and long-term human health. Conventional toxicology provides an indispensable foundation for food safety regulation through hazard characterization and population-based health guidance values but is less equipped to explain interindividual variability in biological response and chronic disease susceptibility. Precision toxicology provides an integrative and mechanism-informed framework that combines high-resolution analytical chemistry, human biomonitoring, exposomics, multiomics, new approach methodologies, and artificial intelligence. This integration enables the characterization of biologically effective exposure, the elucidation of exposure-response relationships, and the identification of interindividual variability in toxicological susceptibility. This perspective proposes a translational framework connecting external exposure → internal dose → biological response → individual susceptibility → health outcome. We position this framework relative to existing exposome, exposure-pathway, and adverse-outcome-pathway frameworks; specify the evidence required at each transition; make its life-course dimension explicit; illustrate it with a worked per- and polyfluoroalkyl substance (PFAS) example; and outline a stepwise route into food risk assessment together with its principal limitations. Such integration could advance food safety science beyond residue detection toward biologically informed exposure assessment, ultimately supporting more evidence-based regulatory decision-making, preventive strategies, and public health protection.},
}

@article {pmid42883703,
year = {2026},
author = {Pérez-Castro, S and Carballo-Quinta, M and Rodríguez-Costas, N and Freire-Rodríguez, A and Davina-Nunez, C and Bellas-Pereira, A and Taboada-Rodríguez, P and Pérez-Schoch, M and Cabrera-Alvargonzález, JJ and Muller-Arteaga, CA and Sánchez-García, JF and Cespón-Outeda, E and López-Díez, ME},
title = {Gut Microbiota Signatures Associated with Metastatic Prostatic Cancer Treated with Androgen Receptor Pathway Inhibitor (ARPI) Therapy.},
journal = {International journal of molecular sciences},
volume = {27},
number = {19},
pages = {},
doi = {10.3390/ijms27198454},
pmid = {42883703},
issn = {1422-0067},
support = {Leonardo de la Peña 2022 Grant//Urological Research Foundation/ ; GAIN IN607B-2022-19//Axencia Galega de Innovacion/ ; },
mesh = {Humans ; Male ; *Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism ; *Gastrointestinal Microbiome/drug effects ; *Androgen Receptor Antagonists/therapeutic use/pharmacology ; *Receptors, Androgen/metabolism ; Neoplasm Metastasis ; Aged ; Disease Progression ; Metagenomics/methods ; },
abstract = {Metastatic prostate cancer (MPCa) remains an aggressive disease despite the introduction of androgen receptor pathway inhibitors (ARPIs), and biomarkers predicting progression are still lacking. The aim of this study was to investigate gut microbiota (GM) composition and functional potential associated with advanced disease and progression under ARPI therapy. The GM of 15 patients with metastatic PCa receiving ARPIs, including 5 patients with disease progression, was compared with that of 39 patients with untreated (UT) PCa using shallow shotgun metagenomic sequencing. The metastatic PCa cohort receiving ADT plus ARPI therapy showed reduced microbial alpha diversity and significant taxonomic and functional differences compared with the untreated, clinically localized PCa reference cohort. In patients with advanced disease, microbial functions related to dietary carbohydrate utilization, fermentation, epithelial interaction, and microbial structural maintenance were predominantly underrepresented, whereas stress-responsive and redox-associated functions were overrepresented. These alterations may reflect reduced metabolic and ecological versatility alongside increased adaptation to host-associated stress conditions. Compared with the UT group, in patients with progression we found that Bifidobacterium longum, Anaerobutyricum hallii, Ruminococcus sp., and Blautia obeum (LinDA coefficients 5.7, 2.6, 2.6 and 2.4, respectively) were enriched, whereas Sutterella wadsworthensis, Butyricimonas, Bilophila wadsworthia, Alistipes indistinctus, and Intestinimonas were depleted (LinDA coefficients -8.4, -5.9, -5, -5 and -3, respectively). Together, these findings identify distinct taxonomic and functional features associated with metastatic PCa under systemic therapy and microbial features observed in patients experiencing progression during ARPI treatment, providing potential candidates for biomarker development and generating testable hypotheses regarding microbiome-host metabolic interactions in treatment resistance. The GM may therefore represent a potential source of biomarkers for advanced PCa and progression under ARPI therapy, although longitudinal and multi-omics studies are required to determine their predictive value and functional relevance.},
}

Humans
Male
*Prostatic Neoplasms/drug therapy/microbiology/pathology/metabolism
*Gastrointestinal Microbiome/drug effects
*Androgen Receptor Antagonists/therapeutic use/pharmacology
*Receptors, Androgen/metabolism
Neoplasm Metastasis
Aged
Disease Progression
Metagenomics/methods