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

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

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

STUDY REGISTRATION NUMBER: ISRCTN15535639.},
}

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

@article {pmid42987833,
year = {2026},
author = {Cho, J and Danner, R and Kim, WS and Lopez, L and Williams, J and Singh, A and Han, JA and Van Vranken, JG and Walker, AS and Rhoads, TW and Chaudhari, SN},
title = {Microbial metabolism of methotrexate produces a STAT3 signaling molecule that alleviates gut inflammation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.10.005},
pmid = {42987833},
issn = {1934-6069},
abstract = {Methotrexate (MTX) is a gold standard therapy for inflammatory diseases but has mixed therapeutic success in inflammatory bowel disease (IBD). The gut microbiota impact MTX efficacy and toxicity by metabolizing MTX and altering its bioavailability, yet how inflammation alters this metabolism, and how the resulting metabolites act on the host, remain poorly understood. Here, we find that gut microbes, notably Clostridium asparagiforme, metabolize MTX via carboxypeptidase G2 (CPDG2) to produce deoxyaminopteroic acid (DAMPA). In intestinal epithelial cells, DAMPA preserves mitochondrial health through mitochondrial signal transducer and activator of transcription 3 (STAT3) signaling and enhances mitophagy. DAMPA administration attenuates intestinal inflammation in vivo, and remodels colonic mitochondrial pathways. IBD mouse models show reduced microbial CPDG2 and DAMPA, while patients with IBD show reduced CPDG2 gene abundance and suppressed DAMPA-enriched mitochondrial pathways, potentially explaining MTX outcomes in IBD. Together, these findings reframe microbial MTX metabolism from passive drug detoxification to active regulation of host mitochondrial and inflammatory homeostasis.},
}

@article {pmid42988189,
year = {2026},
author = {Luque, MVS and Moreno, ASA and Angarita-Planchez, ME and Múnera-Rodríguez, AM and López-Enríquez, S and Casado-Jurado, D and de Miguel, M and Palomares, F},
title = {Hypoxia Orchestrates the Natural History of Inflammatory Bowel Disease: Mechanisms and Therapeutic Opportunities.},
journal = {Pharmacological research},
volume = {},
number = {},
pages = {109736},
doi = {10.1016/j.phrs.2026.109736},
pmid = {42988189},
issn = {1096-1186},
abstract = {Inflammatory bowel disease (IBD) arises from a dynamic interplay between epithelial dysfunction, immune activation, microbial dysbiosis and tissue remodelling. Although hypoxia was initially regarded as a consequence of intestinal inflammation, it is now recognized as an active regulator of epithelial, immune and stromal responses that coordinate disease progression. Here, we propose that hypoxia acts as a biological organizer linking oxygen sensing to the transition from intestinal homeostasis to chronic inflammation and structural tissue damage. We use this term in a mechanistic rather than a hierarchical sense: oxygen availability is a shared upstream constraint on epithelial, immune, microbial and stromal programmes, not a single initiating event. This review integrates evidence connecting oxygen sensing with epithelial barrier integrity, immunometabolism, microbial ecology and stromal remodelling, with emphasis on advances in single-cell transcriptomics, spatial biology and microbiome research. Physiological low-oxygen gradients support epithelial metabolism, barrier integrity and immune tolerance, whereas persistent inflammatory hypoxia drives oxidative stress, metabolic reprogramming and maladaptive epithelial-immune-microbial interactions. Hypoxia also contributes to spatially distinct epithelial, immune and stromal niches that may sustain chronic inflammation and fibrotic progression. Microbial metabolites, including short-chain fatty acids and succinate, together with iron metabolism and ferroptosis, further link oxygen sensing to tissue injury, adaptation and repair. These findings position hypoxia-responsive signalling as a pharmacologically actionable network rather than a downstream consequence of inflammation. Targeting selected components may promote mucosal healing and limit structural disease progression, although successful translation will require cell- and isoform-selective modulation, adequate tissue exposure and careful assessment of long-term safety.},
}

@article {pmid42988284,
year = {2026},
author = {Pourbozorg, G and Heckmann, ND and Mont, MA and Lieberman, JR and Parvizi, J},
title = {Can We Target the Microbiome to Improve Outcomes in Osteoarthritis and Arthroplasty?.},
journal = {The Journal of arthroplasty},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.arth.2026.10.044},
pmid = {42988284},
issn = {1532-8406},
abstract = {Osteoarthritis (OA) is the most prevalent degenerative joint disease and a leading cause of pain, disability, and joint arthroplasty worldwide. Despite advances in surgical technique and perioperative care, periprosthetic joint infection (PJI) remains a devastating complication associated with substantial morbidity, mortality, and healthcare costs. Increasing evidence suggests that the gut microbiome plays a central role in regulating systemic inflammation, immune competence, metabolic homeostasis, and intestinal barrier integrity, biological processes relevant to both OA progression and postoperative infection risk. Preclinical and emerging clinical studies support the existence of a gut-joint axis, whereby alterations in gut microbial composition and microbial metabolites, such as short-chain fatty acids (SCFAs), bile acids, lipopolysaccharides, tryptophan-derived metabolites, and other immunomodulatory compounds, influence joint inflammation, cartilage degeneration, and host immune responses. Experimental models demonstrate that dysbiosis exacerbates OA-related joint damage, while targeted modulation of the gut microbiome can attenuate inflammation, reduce oxidative stress, and preserve cartilage integrity. Importantly, perioperative factors such as surgical stress, antibiotic exposure, and nutritional changes may further disrupt gut microbial homeostasis, potentially impairing immune resilience and increasing susceptibility to PJI. Microbiome-targeted strategies, including dietary modification, probiotics, prebiotics, and physical activity, have shown promise in restoring microbial balance and supporting immune regulation in arthritic populations. Although most evidence remains preclinical or observational, these findings suggest that modulation of the gut microbiome represents a biologically plausible adjunctive approach for both osteoarthritis management and perioperative optimization. This review summarizes current evidence linking the gut microbiome to OA pathophysiology and surgical outcomes and evaluates the potential role of microbiome modulation in joint health optimization and PJI risk reduction. Although biologically compelling, current evidence remains largely preclinical and observational, and prospective clinical trials are required before routine implementation.},
}

@article {pmid42988299,
year = {2026},
author = {Hua, J and Pi, X and Zhang, J and Tian, J and Sun, X and You, X and Sun, C and Li, Y and Li, M and Liu, Q and Liu, L and Liu, R and Luo, X and Li, F and Zheng, H},
title = {Feedstock-specific biochar attenuates brominated flame retardant transfer to cherry radish: Links to rhizosphere microbiome reassembly and dietary exposure reduction.},
journal = {Environmental research},
volume = {},
number = {},
pages = {126113},
doi = {10.1016/j.envres.2026.126113},
pmid = {42988299},
issn = {1096-0953},
abstract = {Brominated flame retardants (BFRs) are emerging contaminants in agricultural soils that threaten food safety and human health. Although biochar can remediate contaminated soils, its performance and mechanisms in soil-root vegetable systems remain unclear. Herein, the effects of biochars from pig manure (PHC), peanut shell (FSC), corn straw (STC), and bamboo (BBC) on soil-to-food transfer and dietary exposure of decabromodiphenyl ether (BDE-209) and pentabromotoluene (PBT) were investigated in a 48-day pot experiment with bacterial and fungal community analyses. PHC, FSC, and BBC reduced BDE-209 and PBT accumulation in cherry radish by 60.1-78.3% and 34.1-89.4%, respectively, relative to the control. These biochars enriched putative BFR-attenuating taxa (Pseudomonas, Sphingomonas, and Humicola); enrichment of oxygen-containing functional groups (C=O and O-C=O) and dissolved organic matter in these biochars may have provided high-affinity niches that selectively recruited these taxa, potentially contributing to lower BFR accumulation. PHC, FSC, and BBC also promoted deterministic fungal assembly and more complex, stable networks. Overall, BFR transfer to cherry radish was associated with feedstock-dependent biochar properties, plant performance, and rhizosphere community assembly, providing an integrated basis for selecting biochars for contaminated agricultural soils. These findings link soil, rhizosphere, and food exposure and support feedstock-specific biochar use to reduce contaminant transfer while improving rhizosphere ecological health.},
}

@article {pmid42988334,
year = {2026},
author = {Dong, Z and Ye, Q and See, WC and Oo, A and Pan, M},
title = {Advances in engineering strategies for manipulating insect antiviral immunity.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101648},
doi = {10.1016/j.cois.2026.101648},
pmid = {42988334},
issn = {2214-5753},
abstract = {Insect immunity primarily relies on a highly developed innate immune system to defend against viral invasion. Research on insect immunity has gained considerable traction in recent years, with major progress in elucidating the underlying immune and defense mechanisms and developing improved pest-control strategies. Collectively, these advancements have paved a translational pathway toward the close application of insect immunology in fields such as medicine, agriculture, and ecology. This review systematically discusses current progress in genetic engineering-based strategies for modulating insect antiviral immunity, specifically transgenic, antimicrobial peptides, gene-editing gene drives, and microbiome regulation. The review also outlines the implications of regulating insect immunity for enhancing genetic traits, preventing disease, controlling vectors, and modifying pathogenic microorganisms.},
}

@article {pmid42988415,
year = {2026},
author = {Leung, JM},
title = {Unravelling the mysteries of long COVID: what the microbiome can tell us.},
journal = {The European respiratory journal},
volume = {68},
number = {5},
pages = {},
doi = {10.1183/13993003.01419-2026},
pmid = {42988415},
issn = {1399-3003},
}

@article {pmid42988675,
year = {2026},
author = {Kuribayashi, R and Nakano, A and Kawasaki, M and Hariu, A and Sakurai, A},
title = {Regulatory science for microbiome-based medicines: lessons from Pharmaceuticals and Medical Devices Agency initiatives.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.10.007},
pmid = {42988675},
issn = {1879-3096},
abstract = {Recent Pharmaceuticals and Medical Devices Agency initiatives for live biotherapeutic products, fecal microbiota transplantation, and phage therapy medicinal products illustrate a dialog-driven regulatory approach for microbiome-based medicines. We compare this strategy with evolving Food and Drug Administration and European Medicines Agency frameworks and identify priorities for future regulatory development and international alignment.},
}

@article {pmid42988683,
year = {2026},
author = {Brown, BRP and Dahlquist, SE and Miranker, AD},
title = {Microbiome sharing and the shift to relational privacy.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.007},
pmid = {42988683},
issn = {1878-4380},
abstract = {Concerns about big data privacy are growing. While much of the current privacy framework focuses on individuals, protections must also account for relational risks. In this article, we use the microbiome as an example to demonstrate the limitations of applying existing individual-centered privacy frameworks to biological data that can reveal information about interacting individuals.},
}

@article {pmid42988772,
year = {2026},
author = {Asoudeh-Fard, A and Barzegari, A and Maghsoodi, M and Gholami, A},
title = {Harnessing Nanotechnology and Microbiome Interactions to Enhance Therapeutic Outcomes in GI Cancers.},
journal = {Expert reviews in molecular medicine},
volume = {},
number = {},
pages = {1-53},
doi = {10.1017/erm.2026.10087},
pmid = {42988772},
issn = {1462-3994},
}

@article {pmid42988933,
year = {2026},
author = {Nap, B and Hensen, T and Barton, W and Sheehy, A and Widder, J and Chenna, S and Thiele, I},
title = {Personalization and evaluation of human whole-body metabolic models and community microbiome models using Persephone.},
journal = {Nature protocols},
volume = {},
number = {},
pages = {},
pmid = {42988933},
issn = {1750-2799},
abstract = {Human metabolism and human gut microbiome co-metabolism can be difficult to investigate in vivo owing to the complexity of the systems involved. Genome-scale metabolic modeling with human whole-body metabolic models (WBMs) offers a computational approach to address this challenge. However, personalization and analysis of WBMs requires comprehensive knowledge of metabolic modeling, which can be daunting for beginners. To reduce the computational expertise required and to standardize the process of working with and analyzing WBMs, we present Persephone: a personalization and evaluation pipeline for human WBMs. Persephone has functionalities to create community microbiome models from raw sequencing data or taxonomy-assigned read tables, use physiological and metabolomic data to create personalized WBMs, combine community microbiome models with WBMs or personalized WBMs to create community microbiome (personalized) WBMs, optimize WBMs according to user-defined metabolic reactions, perform statistical analyses to describe the data, and visualize significant results in various figures. Persephone saves intermediate results as well as a log file with all changes made to the model, data and any warnings encountered during the various steps. Persephone is designed for use by anyone with basic research-computing experience and access to modest computer hardware. Applications include the investigation of human-microbiome co-metabolism and the evaluation of the effects of various physiological parameters, such as weight, on human metabolism. Using a dataset of 100 metagenomic samples, it can take several days to a week to run Persephone on a single computer, depending on the number of reactions optimized and whether taxonomic assignment is performed.},
}

@article {pmid42988934,
year = {2026},
author = {Nagata, N and Wei, R and Kaneko, G and Nishijima, S and Aoki, R and Kojima, Y and Tamura, Y and Sugiyama, M and Hamabata, T and Nakagawa, T and Ueki, K and Ohsugi, M and Nakanishi, Y and Ito, A and Asami, S and Suzuki, R and Kuhn, M and Bork, P and Hattori, M and Ohno, H and Uemura, N},
title = {Opposing microbiome-mediated axes link modifiable lifestyles to health and chronic diseases.},
journal = {Nature medicine},
volume = {},
number = {},
pages = {},
pmid = {42988934},
issn = {1546-170X},
support = {28-2401, 19A1011, 24A1010//National Center for Global Health and Medicine (NCGM)/ ; 24A1010//National Center for Global Health and Medicine (NCGM)/ ; 28-2401//National Center for Global Health and Medicine (NCGM)/ ; NA//Smoking Research Foundation (SRF)/ ; NA//Takeda Science Foundation/ ; JP22fk0410051, JP22fk0108538, JP25ck0106061//Japan Agency for Medical Research and Development (AMED)/ ; },
abstract = {Analyses disentangling the role of the gut microbiome in linking lifestyle factors to health outcomes remain limited. Here, using fecal shotgun metagenomics from 6,803 adults in the Japanese 4D cohort, we identified two opposing microbiome-mediated axes linking lifestyle to health and 15 diseases. A health-associated axis enriched in microbial metabolism of dietary components was linked to plant-based, soy and dairy intake. In contrast, a disease-associated axis, enriched in oral-derived bacteria and pathobionts, was linked to refined carbohydrates and sedentary behavior. Starter culture microorganisms used to ferment foods did not show statistically significant mediation of the observed health effects. Alcohol was associated with both health- and disease-oriented mediation patterns involving microbial host-glycan utilization. Microbiome-defined health- and disease-oriented mediator axes were supported by fecal short-chain fatty acids and plasma cytokines from >1,700 individuals, revealing butyrate-associated anti-inflammatory and pro-inflammatory host profiles, respectively. Microbiome-based prediction (MADE) scores captured lifestyle-microbiome-disease mediation patterns and distinguished individual diseases across 13 independent external cohorts from the United States, China, Sweden, Russia and Australia. We identify the gut microbiome as a key mediator linking lifestyle to health and disease, providing a framework for microbiome-based assessment to guide lifestyle interventions for health promotion and disease prevention.},
}

@article {pmid42989114,
year = {2026},
author = {Saha, P and Böttcher, L and Gonze, D and Zhou, X and Bernaerts, K and Faust, K},
title = {Effects of common antibiotics on representative gut bacterial strains associated with inflammatory bowel disease.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42989114},
issn = {1471-2180},
support = {G046721N//Fonds Wetenschappelijk Onderzoek/ ; 1140026N//Fonds Wetenschappelijk Onderzoek/ ; },
mesh = {*Anti-Bacterial Agents/pharmacology ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Escherichia coli/drug effects/growth & development ; *Bacteria/drug effects/growth & development ; *Gastrointestinal Microbiome/drug effects ; Bacteroides fragilis/drug effects/growth & development ; Microbial Sensitivity Tests ; },
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD), a group of multifactorial diseases marked by chronic inflammation of the gastrointestinal tract, is characterized by an altered gut microbial community composition that is enriched in opportunistic and pathogenic species, such as Bacteroides fragilis and adherent-invasive Escherichia coli strains. To better understand the consequences of using antibiotics to suppress these harmful species, we quantified the response of three bacterial species representative of a healthy gut microbiome, as well as two species typically enriched in IBD to five selected antibiotics that are widely employed against anaerobes.

RESULTS: We found that the adherent-invasive Escherichia coli LF82 strain and the type strains of the opportunistic Bacteroides species B. fragilis and B. thetaiotaomicron are resistant to even high doses of several of the tested antibiotics whereas the type strains of the probiotic butyrate producer Roseburia intestinalis and the acetogen Blautia hydrogenotrophica are sensitive to the majority of the tested antibiotics at low concentrations. We performed a Bayesian parameter estimation of a parsimonious mechanistic growth model. The effects of the antibiotics on lag phase, growth rate, and death rate varied across compounds in a manner consistent with their modes of action. For example, metronidazole, which inhibits DNA synthesis, reduced the growth rate, whereas meropenem, which inhibits cell wall synthesis, increased the death rate in several cases. In contrast, eravacycline, piperacillin/tazobactam and rifampin exhibited variable and species-dependent effects on the growth dynamics.

CONCLUSION: The observation that opportunistic strains in monoculture are resistant to several tested antibiotics in contrast to commensals questions the use of broad-spectrum antibiotics for microbiome modulation in gastrointestinal diseases and motivates the need for targeted strategies to reshape dysbiotic microbial communities.},
}

*Anti-Bacterial Agents/pharmacology
Humans
*Inflammatory Bowel Diseases/microbiology
Escherichia coli/drug effects/growth & development
*Bacteria/drug effects/growth & development
*Gastrointestinal Microbiome/drug effects
Bacteroides fragilis/drug effects/growth & development
Microbial Sensitivity Tests

@article {pmid42989121,
year = {2026},
author = {Suchet, M and Pannetier, P and Danion, M and Braunbeck, T and Alves Gomes, P and Cachot, J and Bellec, L},
title = {Long-term intermittent exposure to fluoride and tebuconazole alters gill, skin and gut microbiomes in rainbow trout (Oncorhynchus mykiss).},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42989121},
issn = {1471-2180},
support = {ANSES-22-EST-050//French National Research Program for Environmental and Occupational Health of ANSES/ ; },
mesh = {Animals ; *Oncorhynchus mykiss/microbiology ; *Gills/microbiology/drug effects ; *Triazoles/toxicity/adverse effects/pharmacology ; *Fluorides/adverse effects/pharmacology ; *Bacteria/classification/genetics/drug effects/isolation & purification ; *Gastrointestinal Microbiome/drug effects ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology/drug effects ; *Water Pollutants, Chemical ; Skin Microbiome ; *Microbiota/drug effects ; },
abstract = {BACKGROUND: Fluoride and tebuconazole are two compounds widely used in industrial processes and agriculture, respectively, and are regularly detected in surface waters. Therefore, there is an urgent need to characterise their effects on aquatic organisms. In this context, adopting a holistic approach that integrates the host and its associated microbiomes, the holobiont, is particularly relevant. In this study, rainbow trout were exposed from 6 days post-fertilisation for 7 months to a daily 7-hour pulsed regime of two concentrations of fluoride (6.8 or 24.7 mg/L, representing environmentally relevant levels for contaminated hotspots), to tebuconazole (51.7 µg/L, within the range of agricultural runoff peaks), or maintained in control conditions. At the end of the exposure period, gill, skin and intestine microbiomes were characterized using 16 S rRNA gene metabarcoding.

RESULTS: Fluoride and tebuconazole significantly affected the bacterial alpha diversity in gill and skin tissues. Beta diversity was significantly affected in gill and skin tissues, whereas the intestine exhibited a weak overall treatment effect without significant pairwise differences. If compared to the control treatment, fluoride exposure altered microbial co-occurrence networks, affecting bacterial interconnections in a tissue-specific manner, with reduced interconnections in gills and increased interconnections in skin and intestine compared to the control treatment. Shifts in taxonomical composition were present following exposure to both pollutants, and notably increases in the relative abundance of fish pathogens such as Candidatus Piscichlamydia, Flavobacterium and Aeromonas were observed. Increased abundance of Aeromonas (gill, skin and intestine) and Acidovorax (gill), along with functional predictions, suggested potential alterations in pathways related to antibiotic resistance, warranting further metagenomic investigation.

CONCLUSIONS: These results highlight alterations of gill, skin and intestine microbiomes in the rainbow trout following chronic exposure to fluoride and tebuconazole, with distinct and tissue-specific microbial responses. Beyond taxonomical shifts, the observed alterations of bacterial co-occurrence networks, enrichment of pathogenic bacteria, and antibiotic-resistant taxa, indicating that the fish microbiome is a sensitive bioindicator of chronical chemical stress. Whether these microbial shifts translate into adverse host health outcomes remains to be investigated in future studies.},
}

Animals
*Oncorhynchus mykiss/microbiology
*Gills/microbiology/drug effects
*Triazoles/toxicity/adverse effects/pharmacology
*Fluorides/adverse effects/pharmacology
*Bacteria/classification/genetics/drug effects/isolation & purification
*Gastrointestinal Microbiome/drug effects
RNA, Ribosomal, 16S/genetics
Skin/microbiology/drug effects
*Water Pollutants, Chemical
Skin Microbiome
*Microbiota/drug effects

@article {pmid42989307,
year = {2026},
author = {Jacot, W and Cayrefourcq, L and Dunyach-Remy, C and Jarlier, M and Lossaint, G and D'Hondt, V and Pastre, T and Garima, F and Massemin, B and Guiu, S and Dupuy, AMG and Cristol, JP and Lavigne, JP and Alix-Panabières, C},
title = {Circulating blood microbiome biomarkers as liquid biopsy in breast cancer.},
journal = {Journal of experimental & clinical cancer research : CR},
volume = {45},
number = {1},
pages = {},
pmid = {42989307},
issn = {1756-9966},
support = {No. 25014115//FEDER/ ; No. 115749//CANCER-ID program/ ; Recherche Tremplin' initiative//Centre Hospitalier Régional Universitaire de Montpellier/ ; },
mesh = {Humans ; Female ; *Breast Neoplasms/blood/pathology/microbiology ; Liquid Biopsy/methods ; *Biomarkers, Tumor/blood ; Prognosis ; Middle Aged ; Neoplastic Cells, Circulating/pathology ; *Microbiota ; Adult ; Aged ; },
abstract = {BACKGROUND: Circulating tumor material can already be used to help in cancer management, but host-microbiota interactions may add complementary value. This study evaluated a "liquid microbiopsy", combining cell-free microbial DNA (cf-mbDNA) with host biomarkers of microbial translocation/permeability (LBP, sCD14, I-FABP), to refine staging and prognosis in breast cancer.

METHODS: We analyzed 136 individuals: 58 metastatic breast cancer (MBC), 58 early breast cancer (EBC), and 20 healthy donors. Plasma cf-mbDNA was quantified by 16S rRNA qPCR with extraction/run negative controls; LBP, sCD14, I-FABP by ELISA; and CRP by immunoturbidimetry. Circulating tumor cells (CTCs) and PD-L1 on CTCs were assessed by CellSearch® and immunostaining. Diagnostic performance was assessed by area under the ROC curve. In MBC, progression-free survival (PFS) and overall survival (OS) were analyzed using Kaplan-Meier and Cox models.

RESULTS: LBP discriminated EBC from MBC with an AUC 0.92, with a slight improvement in the 3- or 5-marker models (AUC 0.936-0.939). For EBC vs healthy donors, CRP showed modest performance (AUC 0.73), and marker combinations offered no improvement.. In MBC (median follow-up 77.5 months), median PFS and OS were 4.5 and 14.5 months, respectively. In univariate analysis, shorter PFS was associated with tumor subtype, > 3 prior treatments, > 2 metastatic sites, CTCs ≥ 5, and PD-L1-positive CTCs detection. In multivariate analysis, sCD14 and I-FABP independently predicted PFS, while sCD14 was independently associated with OS.

CONCLUSIONS: A measurable host-microbiota-barrier axis (LBP, sCD14, I-FABP) provided stage-related and prognostic information complementary to CTC/PD-L1 status, whereas cf-mbDNA load alone showed limited discriminative value. These findings support liquid microbiopsy as a complementary extension of liquid biopsy but must be considered as exploratory, and warrant multicenter validation in larger independent cohorts with standardized pre-analytics and low-biomass controls.

TRIAL REGISTRATION: NCT03449264; NCT02866149.},
}

Humans
Female
*Breast Neoplasms/blood/pathology/microbiology
Liquid Biopsy/methods
*Biomarkers, Tumor/blood
Prognosis
Middle Aged
Neoplastic Cells, Circulating/pathology
*Microbiota
Adult
Aged

@article {pmid42989337,
year = {2026},
author = {Barón, MD and Martín-Vivaldi, M and Martínez-Renau, E and Arlettaz, R and Engelbrecht, D and Enkvist, C and van Rensburg, ELJ and Zhang, L and Martín-Platero, A and Martínez-Bueno, M and Martínez-García, Á and Ruiz-Castellano, C and Schaub, M and Stanback, M and van de Ven, TMFN and Videvall, E and Liang, W and Soler, JJ},
title = {Functional phylosymbiosis in birds: phylogeny and antimicrobial properties of bacterial symbionts in Bucerotiformes.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42989337},
issn = {2524-4671},
abstract = {Bacterial symbionts and their animal hosts differ in the strength and type of selection pressures that promote their evolution and, as some host traits are phylogenetically conserved, their symbiotic bacterial communities could also exhibit greater similarity than expected by chance; a pattern known as phylosymbiosis. This might result from differences in bacterial assemblages across species-specific habitats, and/or from natural selection favouring host traits that allow harbouring functional species-specific bacteria (functional phylosymbiosis). We explored these patterns in eight Bucerotiformes taxa, including hoopoes, woodhoopoes, and hornbills, of which hoopoes and woodhoopoes harbour antibiotic-producing symbionts in their uropygial gland. We characterised uropygial secretion bacterial communities using high-throughput 16S-rRNA gene sequencing and analysed its association with avian phylogeny. Furthermore, we quantified antimicrobial activity of bacterial isolates, and explored its relationship with host phylogenetic distances and bacterial community composition. We found a significant correlation between avian phylogeny and bacterial community dissimilarities, supporting phylosymbiosis. Moreover, antimicrobial activity was significantly predicted by bacterial community composition and the relative abundance of particular strains in hoopoes and woodhoopoes. These findings suggest that antimicrobial properties of symbionts could be responsible for the detected phylosymbiosis and that natural selection may favour uropygial gland features allowing hosts to harbour specific antimicrobial-producing symbionts.},
}

@article {pmid42989368,
year = {2026},
author = {Ma, B and Xiao, J and Xu, Y and Chen, T and Liu, S and Zou, S and Gao, D and Zhuang, Y and Li, M and Wang, W and Li, S and Cao, Z},
title = {Multi-omics analysis reveals microbial and metabolic signatures associated with neutral detergent fiber digestibility in dairy cattle.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42989368},
issn = {1674-9782},
support = {No: 2025-JSGG-048//National Technology Innovation Center for Dairy/ ; No: 2024BBF01006//Key R&D Programme of Ningxia/ ; },
abstract = {BACKGROUND: The rumen microbiome is central to fiber degradation in dairy cows, yet the precise functional and metabolic networks driving variations in neutral detergent fiber (NDF) digestibility remain poorly understood. Elucidating these microbiome-host interactions is critical for improving forage utilization and advancing sustainable dairy production.

RESULTS: Employing an integrative metagenomics-metabolomics approach, we characterized the rumen microecology of lactating dairy cows exhibiting high and low NDF digestibility phenotypes (n = 10/group). Metagenomic profiling revealed a significant enrichment of fibrolytic taxa (Prevotella sp., Lachnospiraceae bacterium) and carbohydrate-active enzymes in the high-NDF group (HI). In addition, species-level differential abundance testing showed that Methanobrevibacter spp. was more abundant in the low-NDF group (LO) than in the HI group, whereas no archaeal differences were detected at the phylum or genus levels. Functional and metabolomic analyses indicated broader enrichment of amino acid degradation functions and higher concentrations of major volatile fatty acids (VFAs) in HI cows, consistent with stronger overall ruminal fermentation activity. Furthermore, VFAs and microbial composition explained 54.3% and 43.0% of the variation in NDF digestibility, respectively. An exploratory machine learning model based on selected annotated metabolite features showed moderate discriminatory performance, with an out-of-bag accuracy of 77.19%.

CONCLUSIONS: Our findings suggest that coordinated shifts in rumen microbial composition, amino acid metabolism, and VFA production are associated with variation in NDF digestibility in dairy cattle. These results provide a basis for future studies aimed at improving fiber utilization through microbiome-informed nutritional or breeding strategies.},
}

@article {pmid42989377,
year = {2026},
author = {Lad, H and Shah, A and Thompson, ER and Javid, S and Chee, RH and Zaransky, S and Dhanda, A and Mudhar, A and Lamichhane, S and Chua, AT and Bono, K and Bono, J and Kaye, R and Johnson, WE and Cugini, C and Yan, K},
title = {Laryngeal Cancer Microbiome Study Reveals Parvimonas and Campylobacter as Potential Therapy Targets.},
journal = {The Laryngoscope},
volume = {},
number = {},
pages = {},
doi = {10.1002/lary.71027},
pmid = {42989377},
issn = {1531-4995},
support = {PC 162-25//New Jersey Health Foundation/ ; },
abstract = {OBJECTIVE: Laryngeal cancer accounts for 40% of head and neck malignancies and 1% of all cancer-related deaths worldwide. We evaluated the laryngeal cancer microbiome to identify cancer-specific genera as potential treatment targets.

METHODS: A prospective study was conducted using 57 laryngeal mucosal samples from 24 treatment-naive laryngeal cancer patients and 33 patients who were undergoing otolaryngological surgery unrelated to oral or laryngeal diseases (01/2023-09/2025). DNA was extracted and amplified in triplicate, targeting the V3/V4 region of the 16S rRNA gene, followed by paired-end 2 × 300 bp sequencing on the Illumina NextSeq 2000. Amplicon sequence variants were identified via DADA2 and assigned to genera using a naive Bayes classifier. Two samples with zero classified read pairs were excluded.

RESULTS: Most patients were male (87.5% cancer, 66.7% controls) and smokers (83.3% cancer, 54.5% controls). Cancer patients' core laryngeal microbiomes uniquely contained Parvimonas (3.67%; 95% CI: 0.70%-6.64%), and Campylobacter (1.12%; 95% CI: 0.60%-1.63%), while control patients' uniquely contained Corynebacterium (2.97%; 95% CI: 0.00%-7.67%) and Alloprevotella (1.34%; 95% CI: 0.64%-2.04%). Cancer samples were significantly enriched in 19 genera, notably Peptococcus (2.93, q = 0.0003), Campylobacter (1.68, q = 0.009), and Parvimonas (2.02, q = 0.03), compared to controls.

CONCLUSIONS: Laryngeal cancer patients' samples displayed microbial dysbiosis, with enrichment of microbes present in gastrointestinal cancers, cervical cancer, and inflammatory states; they also exhibited loss of immunoprotective taxa. These findings support that microbiome profiling can distinguish malignant mucosa and guide future studies targeting genera increased in cancer, including Parvimonas and Campylobacter.},
}

@article {pmid42989406,
year = {2026},
author = {Shen, H and Ma, L and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Microbial drivers of high aquaculture productivity: decoupling of taxonomic and functional profiles enables efficient nitrogen cycling in greenhouse shrimp farming.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42989406},
issn = {2524-4671},
support = {NWZZJ2025-2027-05//Major Project of Hubei Agricultural Microbial Industry Development-Innovative Bio-feed Development and Demonstration of Straw-Based Feed Utilization/ ; },
abstract = {As a global cornerstone of animal protein, farmed shrimp production in China has been revolutionized by the Greenhouse Shrimp Farming Model (GSFM). However, the microbial mechanisms underpinning the productivity and biosafety of this intensive paradigm remain poorly understood. Through a large-scale metagenomic survey of 90 standardized aquaculture units in the core GSFM production regions of China, spanning a 15-degree latitudinal gradient, we deciphered the functional architecture of the GSFM microbiome. Our results reveal a striking functional convergence despite geographic taxonomic variation: while microbial compositions shifted across regions, the core metabolic pathways-particularly those governing nutrient cycling-remained conserved. High-productivity systems, notably in southern provinces (Guangxi and Guangdong), were characterized by a specialized microbial repertoire that optimized water chemistry through efficient nitrogen processing. We identified a sophisticated spatial division of labor, where the gut microbiota acts as a specialized nitrite detoxification unit, while the water column microbiota serves as the primary engine for ammonia assimilation. Furthermore, we characterized a diverse antibiotic resistome and utilized host-tracking to evaluate the ecological costs of intensification. These findings shift the focus from microbial identity to functional niche partitioning, providing a mechanistic blueprint for the sustainable intensification of aquaculture through targeted microbiome management.},
}

@article {pmid42989411,
year = {2026},
author = {Jahnke, TT and Holschuh, C and Schlattmann, P},
title = {Mediterranean diet and risk of prostate cancer: a systematic review and meta-analysis of observational studies.},
journal = {BMC nutrition},
volume = {12},
number = {1},
pages = {},
pmid = {42989411},
issn = {2055-0928},
abstract = {BACKGROUND: Prostate cancer is the most common malignancy among men worldwide. In addition to non-modifiable risk factors, modifiable lifestyle factors are increasingly recognized in prevention. The Mediterranean diet (Med Diet), characterized by high intake of plant-based foods, unsaturated fatty acids, and antioxidant micronutrients, has been proposed as a protective dietary pattern.

METHODS: A systematic search was conducted in PubMed, Web of Science, and Scopus examining associations between Mediterranean diet adherence and prostate cancer risk. Fourteen studies met eligibility criteria. Meta-analysis was performed in R applying a random-effects model (REML estimation; Hartung-Knapp adjustment). Heterogeneity was assessed with I² and τ²; publication bias was evaluated using a funnel plot, contour-enhanced funnel plot, and Egger's test.

RESULTS: Based on a random effects model, we did not find a statistically significant difference in risk of prostate cancer in men with high versus low Mediterranean diet adherence (RR = 0.98; 95% CI: 0.93-1.04). Heterogeneity was moderate (Q = 19.95, I² = 34.8%). Although Egger's regression test did not indicate statistically significant publication bias (p = 0.115), complementary analyses (Q-Q plot and limit meta-analysis) suggested a possible small-study effect, warranting cautious interpretation.

CONCLUSION: In this meta-analysis, no protective effect of the Mediterranean diet against prostate cancer was found. Nevertheless, biological plausibility and inconsistent epidemiological trends suggest that further research using standardized dietary assessments and incorporating genetic and microbiome-related factors is needed.

TRIAL REGISTRATION: The review protocol was not prospectively registered.},
}

@article {pmid42989617,
year = {2026},
author = {Sommer, AJ and Kiudeliene, E and Lauridsen, M and Torre, A and Fagan, A and Skieceviciene, J and Jonasson, E and Obolewicz, H and Sikaroodi, M and Kupcinskas, J and Khoruts, A and Gillevet, PM and Bajaj, JS},
title = {Gut‒liver‒brain axis signature of cirrhosis-related cognitive impairment is consistent across multi-national cohorts.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2753908},
doi = {10.1080/19490976.2026.2753908},
pmid = {42989617},
issn = {1949-0984},
mesh = {Humans ; Female ; Middle Aged ; *Liver Cirrhosis/complications/microbiology/psychology ; Male ; Hepatic Encephalopathy/microbiology ; *Gastrointestinal Microbiome ; *Cognitive Dysfunction/microbiology/etiology/physiopathology ; *Liver/metabolism/microbiology/physiopathology ; *Brain/metabolism/physiopathology ; Lithuania ; Mexico ; United States ; Denmark ; Feces/microbiology ; Aged ; Cohort Studies ; Bacteria/classification/isolation & purification/genetics ; *Brain-Gut Axis ; },
abstract = {Cognitive impairment in cirrhosis is associated with an altered gut‒liver‒brain axis, but geographic variations in diet and clinical practices may limit generalizability. We investigated consistency of microbial signatures for cirrhosis-related cognitive impairment across four countries. We enrolled outpatients with cirrhosis from USA, Denmark, Lithuania, and Mexico who underwent Psychometric Hepatic Encephalopathy Score (PHES) testing for covert hepatic encephalopathy (CHE), and stool shotgun metagenomic sequencing. Taxonomic and functional associations with PHES were evaluated after adjustment for MELD, country, demographics, sex, proton pump inhibitor (PPI), lactulose, and rifaximin use. We enrolled 221 patients (median age 58 y, 57.9% men, median MELD 12). Cognitive performance varied by country despite adjustment for clinical covariates. Lithuania demonstrated greater microbial richness and better cognition despite higher MELD, accompanied by distinct dietary patterns including greater yogurt and tea consumption. In the entire cohort, increasing MELD was associated with reduced microbial richness and depletion of commensals. Worse PHES performance, however, showed a distinct microbiome signature with increased Streptococcus abundance independent of MELD, country, PPI use, and HE therapies. Twenty-two microbial pathways were associated with PHES, mostly related to amino-acid biosynthesis and nitrogen metabolism. Of these, ornithine degradation and heme B biosynthesis II were uniquely enriched with worse PHES and CHE, which mapped onto Enterobacteriaceae. We conclude that across four geographically and culturally disparate countries, cirrhosis-related cognitive impairment was associated with consistent microbial compositional and functional alterations distinct from advancing liver disease. These findings support a consistent gut‒liver‒brain axis signature involving oral-gut translocation and altered nitrogen metabolism.},
}

Humans
Female
Middle Aged
*Liver Cirrhosis/complications/microbiology/psychology
Male
Hepatic Encephalopathy/microbiology
*Gastrointestinal Microbiome
*Cognitive Dysfunction/microbiology/etiology/physiopathology
*Liver/metabolism/microbiology/physiopathology
*Brain/metabolism/physiopathology
Lithuania
Mexico
United States
Denmark
Feces/microbiology
Aged
Cohort Studies
Bacteria/classification/isolation & purification/genetics
*Brain-Gut Axis

@article {pmid42989696,
year = {2026},
author = {Pai, N and Nicholson, M and Rich, S and Conrad, MA},
title = {Fecal microbiota transplantation and microbiota-based therapeutics in pediatric clinical practice: Current status and emerging indications.},
journal = {Journal of pediatric gastroenterology and nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1002/jpn3.70633},
pmid = {42989696},
issn = {1536-4801},
support = {//None/ ; },
abstract = {Fecal microbiota transplantation (FMT) is a safe and effective treatment for recurrent or refractory Clostridioides difficile infection (rCDI) in children and adults. This review outlines the evidence behind FMT for rCDI, considerations in special pediatric populations, and limitations in current practice due to FMT access for patients under the age of 18.},
}

@article {pmid42989733,
year = {2026},
author = {Mu, K and Dang, CP and Xue, M and Li, Q and Huynh, HQ and Griffiths, AM and Turner, D and Moayyedi, P and Steinhart, AH and Dieleman, LA and Deslandres, C and Bitton, A and Mack, DR and Jacobson, K and Cino, M and Aumais, G and Panaccione, R and Bressler, B and Lee, SH and Crohn's And Colitis Canada Genetic Environment Microbial Gem Project Research Consortium, and Croitoru, K and Turpin, W},
title = {Fecal neuraminidase correlates with inflammatory signatures and microbiome shifts in preclinical Crohn's disease.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2755166},
doi = {10.1080/19490976.2026.2755166},
pmid = {42989733},
issn = {1949-0984},
mesh = {Humans ; *Crohn Disease/microbiology/enzymology/immunology ; *Neuraminidase/analysis/metabolism ; *Feces/enzymology/chemistry/microbiology ; Female ; Male ; Prospective Studies ; Adult ; *Gastrointestinal Microbiome ; Inflammation ; Bacteria/classification/genetics/isolation & purification/enzymology ; RNA, Ribosomal, 16S/genetics ; Leukocyte L1 Antigen Complex/analysis ; Biomarkers/analysis ; },
abstract = {The mucus layer, rich in mucin glycoproteins, serves as a critical barrier to microbial invasion. Neuraminidases cleave terminal sialic acids from mucin glycans, a process that may influence mucus integrity, epithelial exposure to microbial antigens, and mucosal immune responses, making fecal neuraminidase activity a biologically relevant functional readout of host-microbe interactions in the context of Crohn's disease (CD) pathogenesis. We evaluated whether fecal neuraminidase activity is associated with future CD risk and examine its relationships with inflammatory and microbial signatures relevant to early disease development. Within the prospective GEM cohort, 69 individuals who later developed CD were matched to 69 healthy first-degree relative controls. Fecal neuraminidase activity was measured using a fluorometric assay. Conditional logistic regression assessed its association with future CD risk. Partial Spearman correlations evaluated relationships with 446 serum proteins (OLINK), followed by pathway enrichment analysis, and with fecal calprotectin (FCP) and gut microbial composition (16S rRNA sequencing). Fecal neuraminidase activity was positively associated with future CD (OR = 1.541; 95% CI: 1.05-2.25; p = 0.026). Proteins correlated with neuraminidase activity were enriched in immune and inflammatory pathways. Neuraminidase activity was positively correlated positively with FCP (p ≤ 0.05), and its association with future CD was attenuated after adjustment for FCP. Fourteen microbial taxa were significantly correlated with neuraminidase activity (q ≤ 0.05). Fecal neuraminidase activity's relationships with inflammatory markers and microbial taxa support its potential relevance as a functional marker of host-microbe alterations during preclinical CD.},
}

Humans
*Crohn Disease/microbiology/enzymology/immunology
*Neuraminidase/analysis/metabolism
*Feces/enzymology/chemistry/microbiology
Female
Male
Prospective Studies
Adult
*Gastrointestinal Microbiome
Inflammation
Bacteria/classification/genetics/isolation & purification/enzymology
RNA, Ribosomal, 16S/genetics
Leukocyte L1 Antigen Complex/analysis
Biomarkers/analysis

@article {pmid42989912,
year = {2026},
author = {Pluer, B and Travis, J},
title = {Links Between Environmental Quality, Gut Microbiota, and Host Performance in Nutrient-Impacted Springs.},
journal = {Environmental microbiology},
volume = {28},
number = {11},
pages = {},
doi = {10.1111/1462-2920.70471},
pmid = {42989912},
issn = {1462-2920},
support = {G2020031598770049//Sigma Xia/ ; //Florida State University/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; *Nutrients/analysis ; Florida ; *Natural Springs/chemistry/microbiology ; RNA, Ribosomal, 16S/genetics ; Female ; *Bacteria/classification/genetics/isolation & purification ; Male ; Ecosystem ; *Fundulidae/microbiology/physiology/growth & development ; Reproduction ; Symbiosis ; Fresh Water/chemistry ; },
abstract = {Microbial symbionts may enhance adaptation to environmental stress, yet their role in nutrient-enriched freshwater habitats remains unclear. We conducted a full-factorial laboratory experiment with least killifish, Heterandria formosa, manipulating water chemistry from four Florida springs and gut microbiota inoculations from conspecifics at those sites. Sequencing of 16S rRNA revealed that gut microbial richness was higher in fish reared in less nutrient-loaded waters, but inoculation treatments, if successful, did not produce significant shifts in composition. Gut communities consistently differed from ambient water, with enrichment of Pseudomonadota and Planctomycetota. Females grew more slowly in the most polluted water. In a parallel result, males displayed higher mass-specific metabolic rates in the most nutrient-loaded water. Reproductive output per female nearly doubled when experimental microbiota and water originated from the same site, despite stable microbial diversity, though parentage and inoculation success were not verified; therefore, these results should be interpreted cautiously. These results indicate that environmental quality shapes gut microbiota and host performance, and that matching microbial communities to habitat conditions can boost reproduction. Such interactions may contribute to freshwater fish resilience and merit integration into conservation strategies.},
}

Animals
*Gastrointestinal Microbiome
*Nutrients/analysis
Florida
*Natural Springs/chemistry/microbiology
RNA, Ribosomal, 16S/genetics
Female
*Bacteria/classification/genetics/isolation & purification
Male
Ecosystem
*Fundulidae/microbiology/physiology/growth & development
Reproduction
Symbiosis
Fresh Water/chemistry

@article {pmid42989938,
year = {2026},
author = {Birabaharan, M and Immer, A and Gomez, AN and Valdes, D and Smith, DM},
title = {Mapping HIV reservoir geography: lessons for cure from the Last Gift rapid autopsy cohort.},
journal = {Current opinion in HIV and AIDS},
volume = {},
number = {},
pages = {},
pmid = {42989938},
issn = {1746-6318},
abstract = {PURPOSE OF REVIEW: Deep tissue reservoirs remain a major barrier to HIV cure. Their anatomical distribution and connectivity are difficult to study in living people. We examine how the Last Gift rapid-autopsy cohort clarifies reservoir connectivity, persistence behind anatomical barriers, and variation within organs, and consider the implications for cure.

RECENT FINDINGS: Tissue studies reveal HIV reservoirs that are interconnected across yet differ between and within anatomical sites. Viral sequence analyses suggest that blood links tissue reservoirs, with gut and lymphoid tissues acting as hubs of viral dispersal. Recovery of replication-competent HIV from brain microglia during suppressive antiretroviral therapy (ART) provides direct evidence of a resident brain reservoir. Even within the gastrointestinal tract, HIV DNA burden and transcriptions vary by region, with different microbiome associations in the small and large bowel.

SUMMARY: HIV reservoir geography supports durable ART-free remission as a practical goal. Achieving this goal will likely require combination therapies with complementary functions and tissue access. Because tissue heterogeneity limits what negative biopsies can establish, remission should be assessed through carefully monitored analytical treatment interruption and long-term follow up.},
}

@article {pmid42989971,
year = {2026},
author = {Chai, X and Yan, W and Wei, L and Ning, L and Gao, C and Zhang, Y and Cuo, P and Wang, R and Yang, M and Wang, H},
title = {Multi-Omics Reveals Divergent Gut Microbiome-Metabolome Associations Between High-Altitude Snowcock and Low-Altitude Pheasant.},
journal = {Animal genetics},
volume = {57},
number = {6},
pages = {},
doi = {10.1002/age.70231},
pmid = {42989971},
issn = {1365-2052},
support = {31802256//National Natural Science Foundation of China/ ; 25JRRA653//Natural Science Foundation of Gansu Province/ ; //Gansu Province's Longyuan Young Talents/ ; 2025KJZC00020//Science and Technology Support Special Project of Lanzhou Chengguan District/ ; GSJKKY2025-01//Disease Prevention and Control Research Project of Gansu Province/ ; },
mesh = {Animals ; *Altitude ; *Metabolome ; *Galliformes/microbiology/metabolism/genetics ; Multiomics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Metabolomics ; Bacteria/classification/genetics ; },
abstract = {The gut microecological differences associated with high-altitude habitats remain poorly understood. The Snowcock (Tetraogallus tibetanus), a high-altitude bird endemic to the Qinghai-Xizang Plateau, and the low-altitude Pheasant (Phasianus colchicus) differ strikingly in habitat elevation and diet, providing an ideal comparative model. Fecal samples from six Snowcocks and six Pheasants were analyzed using 16S rRNA gene sequencing and UPLC-MS/MS untargeted metabolomics. Multi-omics integration was performed via Procrustes analysis, correlation networks, and random forest classification. Snowcocks displayed significantly lower alpha diversity and distinct beta diversity clustering compared with Pheasants. The Snowcock microbiota was dominated by Actinobacteriota and enriched in cold-tolerant genera such as Psychrobacillus. In contrast, the Pheasant microbiota showed higher diversity and was dominated by Firmicutes and Bacteroidota. Metabolomics revealed that differential metabolites enriched in Pheasants were predominantly mapped to amino acid metabolism and terpenoid biosynthesis pathways, while those enriched in Snowcocks were linked to glycerophospholipid and sphingolipid metabolism. Multi-omics integration demonstrated a significantly correlated microbiome-metabolome association, and the random forest model discriminated the two species in this dataset. The Snowcock microbiota was simplified and enriched with psychrophilic genera, and its fecal metabolome showed specific glycerophospholipid signatures. These features may reflect microecological divergence associated with the harsh plateau environment. Our findings provide multi-omics insights into high-altitude divergence in wild birds.},
}

Animals
*Altitude
*Metabolome
*Galliformes/microbiology/metabolism/genetics
Multiomics
*Gastrointestinal Microbiome
RNA, Ribosomal, 16S/genetics
Feces/microbiology
Metabolomics
Bacteria/classification/genetics

@article {pmid42990048,
year = {2026},
author = {Syed, RA and Ahmed, A and Hayat, U and Qazi, J},
title = {Targeting the Skin Microbiome in Dermatology: Translational Hype or Emerging Therapeutic Modality?.},
journal = {FASEB journal : official publication of the Federation of American Societies for Experimental Biology},
volume = {40},
number = {21},
pages = {},
doi = {10.1096/fj.202602650RR},
pmid = {42990048},
issn = {1530-6860},
mesh = {Humans ; *Skin Microbiome ; *Skin Diseases/microbiology/therapy ; *Dysbiosis/microbiology/therapy ; Translational Research, Biomedical ; *Dermatology/methods ; *Skin/microbiology ; Probiotics/therapeutic use ; Animals ; *Microbiota ; Prebiotics ; Antimicrobial Peptides ; },
abstract = {The human skin microbiome is a complex network of microorganisms, including bacteria, fungi, viruses, and archaea, that exist in a mutualistic relationship with the host. These microorganisms play important roles in maintaining skin homeostasis, defense against pathogens, regulation of immune response, and antimicrobial peptide synthesis. Dysbiosis, defined as an imbalance of microbial communities, has been linked to dermatological conditions including atopic dermatitis (AD), acne, psoriasis, and chronic wounds. Despite compelling mechanistic insights, the translation of microbiome science into clinically effective therapies remains inconsistent and prematurely optimistic. Emerging therapeutic strategies aim to restore and modulate the skin microbiome with precision, thereby moving beyond conventional broad-spectrum antimicrobial approaches. These encompass probiotics, prebiotics, synbiotics, live biotherapeutic products (LBPs), bacteriophage therapy, microbiome engineering, postbiotics, microbial consortia treatment, and antimicrobial peptides that selectively target microbial communities instead of eliminating them. While these strategies are biologically plausible and have initial-phase evidence, their clinical stability, reproducibility, and scalability are uncertain. Major limitations include inter-individual variability of microbiomes, transient colonization, methodological limitations in functional profiling, and regulatory uncertainties surrounding them. This review article critically evaluates microbiome-directed dermatologic therapies at the crossroads of real therapeutic potential and translational overextension. The field is not just hype; its clinical application has advanced more rapidly than the supporting evidence base justifies. Progress in this domain requires a shift from descriptive and associative research toward mechanism-driven, precision-based interventions. Such interventions must be validated against robust clinical endpoints. By critically assessing biological plausibility, clinical evidence, and translational barriers, this review provides a balanced perspective on the field and outlines realistic pathways for its evolution into a viable therapeutic paradigm.},
}

Humans
*Skin Microbiome
*Skin Diseases/microbiology/therapy
*Dysbiosis/microbiology/therapy
Translational Research, Biomedical
*Dermatology/methods
*Skin/microbiology
Probiotics/therapeutic use
Animals
*Microbiota
Prebiotics
Antimicrobial Peptides

@article {pmid42990228,
year = {2026},
author = {Ferrer, DM and Holton, M and Yang, M and Villamil, I and Urtecho, G},
title = {Culturomics-Guided Precision FMT Enables Stable Antibiotic-Independent Engraftment via Metabolic Niche Targeting.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.25.761671},
pmid = {42990228},
issn = {2692-8205},
abstract = {The gut microbiome's functional architecture can be conceptualized as a network of metabolic niches, yet clinical approaches to fecal microbiota transplantation (FMT) do not leverage niche - level information to guide engraftment. Here, we present a culturomics-based framework that profiles the metabolic niche landscape of individual microbiomes to enable targeted, antibiotic-independent FMT. Using a panel of 60 diverse media conditions, we show that gut communities from genetically identical mice harboring distinct microbiomes exhibit reproducible, vendor - specific niche-occupancy profiles, with each condition selecting for compositionally distinct niche-associated communities (NACs). We demonstrate that antibiotic pretreatment prior to FMT compromises community resilience, yielding communities that lose donor taxa more rapidly and recover less taxonomic diversity after secondary perturbation compared to untreated recipients. By comparing donor and recipient niche profiles, we identify vacant metabolic niches in recipient microbiomes and show that NACs targeting these vacancies achieve stable engraftment persisting for over 72 days without antibiotic pretreatment, whereas NACs targeting occupied niches fail to colonize. Furthermore, complex NACs not only fill vacant niches but reshape the surrounding native community, while simpler NACs engraft with minimal collateral impact. This culturomics-guided framework provides a scalable, mechanistic approach for rational donor-recipient matching that could advance personalized microbiome-based therapies.},
}

@article {pmid42990330,
year = {2026},
author = {Glesener, H and Dorn, N and Cheng, Q and Voth-Gaeddert, LE and Krajmalnik-Brown, R},
title = {Human Gut Microbiota of Healthy Individuals Show Resilience to Acute Aflatoxin B1 Exposure Despite Solvent-Driven Community Shifts.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.26.760590},
pmid = {42990330},
issn = {2692-8205},
abstract = {UNLABELLED: Aflatoxin B1 (AFB1) is a potent mycotoxin linked to severe systemic health issues and gut microbiome disruption in in vivo models. However, it remains unclear whether AFB1 directly impairs human gut microbial composition and function or if observed dysbiosis is host-mediated. The objective of this work was to investigate the direct impact of acute AFB1 exposure on human gut microbiota from healthy individuals using anaerobic batch bioreactors. Fecal inoculum from 17 healthy adults was exposed to AFB1 concentrations ranging from 1,000 to 5,000 ppb, delivered in two solvents (ethanol and corn oil) under conditions simulating the large intestine. Metabolic activity was assessed via short-chain fatty acid (SCFA) and gas production measurements, while community structure was assessed using 16S rRNA gene amplicon sequencing. AFB1 concentrations remained stable throughout the incubations, indicating no significant microbial degradation of AFB1. Results showed that AFB1 did not significantly alter microbial SCFA output or community composition compared to solvent-only controls. Observed shifts in microbial profiles were primarily driven by the solvents used to bring AFB1 into solution rather than by the toxin. These findings demonstrate that healthy human gut microbial communities are resilient to direct, acute AFB1 exposure even at concentrations exceeding typical dietary levels. This suggests that microbiome disruption reported in vivo may be an indirect consequence of host-mediated factors, such as reactive metabolites or systemic immune responses, rather than direct toxicity by the parent compound.

IMPORTANCE: Aflatoxin B1 is a major global health threat, particularly in regions with high dietary exposure, where it is associated with liver cancer and childhood growth stunting. While research has linked aflatoxin exposure to changes in the gut microbiome, the mechanisms driving this "dysbiosis" are not known. This work provides evidence that the parent aflatoxin molecule does not directly affect healthy human gut microbes, even at very high concentrations. The observed resilience of these microbial communities suggests that the damage reported in living organisms is likely caused by host-specific responses to the toxin or by toxic byproducts created during liver detoxification. Furthermore, microbially driven detoxification of the parent aflatoxin molecule was not observed. Distinguishing between direct and indirect toxicity is essential for developing effective strategies and medical interventions to mitigate the health impacts of aflatoxin exposure worldwide.},
}

@article {pmid42990373,
year = {2026},
author = {Noyes, H and Anika, NE and Combs, J and Khan, T and Just, J and Fitzpatrick, S and Angelini, RG and Angelini, DR},
title = {Host specificity, seasonality, and urbanicity shape the gut microbiome of a synanthropic insect.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.28.762591},
pmid = {42990373},
issn = {2692-8205},
abstract = {The soapberry bug Jadera haematoloma is a classic model of rapid adaptive evolution, with a well-documented host shift from native herbaceous sapinds to the introduced goldenrain tree (Koelreuteria spp.). This host shift has facilitated the insect's spread into novel anthropogenic urban habitats. Microbial associations are often critical to insect environmental adaptation. Here, we characterize the gut microbiota of J. haematoloma across native and introduced host plants, seasonal transitions, and a gradient of urbanicity. Our findings indicate that the soapberry bug gut microbiome is highly specialized, with a small number of core bacterial amplicon sequence variants (ASVs) primarily from the families Rhizobiaceae, Streptococcaceae, Enterobacteriaceae, and Lactobacillaceae. While traits such as sex and wing morph do not correlate with microbiome structure, the host plant acts as the primary determinant of community composition. Bugs feeding on the ancestral host plant maintain a more diverse and even microbial community featuring Enterobacteriaceae, whereas the gut environment of bugs on the introduced host is overwhelmingly dominated by a single unclassified Rhizobiaceae ASV. Furthermore, seasonal transitions drive significant turnover among accessory microbial taxa. Finally, we demonstrate that urbanization introduces a distinct ecological effect on the insect's microbiome. While the degree of local green space does not systematically alter within-host taxonomic richness, it is associated with modest change in mean community composition and significantly disrupts microbial community variance. Increased urbanization correlates with significantly higher beta dispersion, indicating that anthropogenic environments lead to more stochastic microbiomes, which may be an indicator of environmental stress. Together, these results illustrate how rapid dietary host shifts and the ecological pressures of urbanization interact to shape the microbiome of a synanthropic insect.},
}

@article {pmid42990397,
year = {2026},
author = {Zandi, E and Medetgul-Ernar, K and Lenz, HJ and Alishahi, F},
title = {Dense Longitudinal Multi-Omics Reveals Microbial-Metabolic-Immune Succession During Immune Checkpoint Therapy.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.24.26366392},
pmid = {42990397},
abstract = {Immune checkpoint inhibitors (ICIs) can induce durable clinical responses, yet relationships among the gut microbiome, microbial function, intestinal metabolism, and host immunity remain incompletely resolved. We performed dense longitudinal multi-omics profiling of a single patient with colorectal cancer metastatic to the liver during ICI therapy and sustained tumor regression. Eleven serial stool samples spanning approximately 7.3 months were analyzed by 16S rRNA sequencing, microbial metatranscriptomics, metabolomics, lipidomics, and stool host-RNA immune profiling and aligned with serial clinical imaging. A major intestinal ecosystem transition accompanied the emergence of clinical response. Microbial abundance and transcriptional activity were frequently discordant, demonstrating that compositional profiling alone incompletely captured microbial dynamics. Taxon-resolved functional analysis revealed sequential microbial states rather than a single responder-associated configuration. Loss of early Bacteroides/Fusobacterium-associated functions accompanied purine/sphingolipid remodeling and changes in myeloid-associated immune signatures. At T5, a transient Bifidobacterium carbohydrate/fermentation program coincided with lactate/indole-3-lactate remodeling and broad adaptive T-cell, memory/regulatory, mucosal, and B-cell immune changes. At T6, marked Clostridium transcriptional emergence and lipid/coenzyme-A pathway activation coincided with fatty-acid/lysophospholipid remodeling and a distinct immune configuration. Historical HUMAnN reconstruction using original UniRef90 and MetaCyc resources confirmed taxon-specific, reaction-associated gene-family support for prioritized functional programs. These findings define a temporally ordered microbial-metabolic-immune succession during ICI response. Although this N-of-1 design cannot establish population generalizability, dense within-person multi-omics resolves transient functional states obscured by cross-sectional analyses and generates testable hypotheses for larger prospective cohorts and personalized studies of ICI response.},
}

@article {pmid42990531,
year = {2026},
author = {Li, R and Fan, X and Kang, J and Huang, X and Shi, Y and Chen, X},
title = {Harnessing metatranscriptomics to unveil the metabolic landscape of microbiota in traditional fermented foods.},
journal = {Current research in food science},
volume = {13},
number = {},
pages = {101601},
pmid = {42990531},
issn = {2665-9271},
abstract = {Traditional fermented foods are widely consumed and valued for their distinctive sensory properties and potential health benefits. These foods contain complex microbiota whose interactions and metabolic activities shape biochemical transformations relevant to product quality, safety, and functionality. Metatranscriptomics provides a culture-independent means of profiling community RNA and examining changes in microbial gene expression during fermentation. However, most fermented-food microbiome studies continue to infer function from community composition or genomic potential rather than from in situ gene expression. Existing metatranscriptomic applications also differ substantially in sampling, RNA processing, sequencing, and data analysis, limiting comparisons across food systems. This review examines the metatranscriptomic workflows applied to fermented foods, including sample preparation, sequencing strategies, and bioinformatic analysis. It identifies practical requirements for reproducible RNA-based studies in complex food matrices and compares transcriptionally represented taxa and pathways across fermentation systems. The review also distinguishes gene expression from realized metabolic activity, an important boundary when interpreting transcript annotations and reconstructed pathways. We further assess the strengths and limitations of metatranscriptomics, both alone and in combination with complementary omics, for resolving microbiota structure-function relationships. Key challenges include data integration, evidence interpretation, and the recovery of biologically meaningful information from complex transcriptomic datasets. When combined with complementary omics and experimental validation, metatranscriptomics can help relate expressed genes and pathways to fermentation phenotypes. These insights may guide the experimental evaluation of starter cultures and the development of more precise fermentation-control strategies.},
}

@article {pmid42990555,
year = {2026},
author = {Sommer, AJ and Sikaroodi, M and Fagan, A and Davis, BC and Khoruts, A and Gillevet, PM and Bajaj, JS},
title = {Global Carriage of Antimicrobial Resistance Genes and Virulence Factors Among Physicians in Cirrhosis Care.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-11319770/v1},
pmid = {42990555},
issn = {2693-5015},
abstract = {Cirrhosis patients are at high risk for drug-resistant infections, which may be transmitted between patients and healthcare providers. In this study, we used shotgun metagenomics to characterize the fecal microbiome of physicians in cirrhosis care (n = 55) across 9 countries. Our results indicate physicians from low- or middle-income countries carry greater antimicrobial resistance gene (ARG) diversity corresponding to increased taxonomic richness. Physicians carried a low prevalence of clinically relevant ARGs or virulence factors (VFs), regardless of country of practice or patient exposure. Further comparison of fecal microbiomes between a subset of cirrhosis patients and physicians' fecal samples collected from the same medical facility in the United States indicated that cirrhosis patients carried a far greater burden of high-risk VFs and ARGs. Collectively, this study provides evidence that most physicians in cirrhosis care are unlikely to be a primary reservoir of drug-resistant pathogens, although further surveillance of healthcare workers is warranted.},
}

@article {pmid42990654,
year = {2026},
author = {Moglowsky, H and Reynolds, C and Lovasz, J and Mir, FM and Shah, M and Varadhan, A and von Dohlen, G and Wall, N and Mahalaha, SA and Blackmon, L and Ringold, SM and Ejaz, FK and Stein, EA},
title = {Evaluation of a Targeted Oral Microbiome Treatment in an Older Adult Population.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.10.27.26366652},
pmid = {42990654},
abstract = {Gingivitis is highly prevalent among older adults and is associated with systemic diseases. Accessible and effective interventions are needed, particularly for underserved populations facing barriers to conventional dental care, such as older adults. This study evaluated the efficacy of a novel, multi-component lozenge (PTx800) designed to modulate the oral environment through blockade of sugar-to-acid and sugar-to-biofilm production of the oral microbiota. A six-week, double-blind, randomized, active placebo-controlled pilot trial was conducted with older adults (final sample n=20) residing in Cleveland, Ohio. Participants were randomized to receive either PTx800 or an active placebo lozenge containing sugar alcohols, used three times daily. Primary outcomes included Modified Gingival Index (MGI), Plaque Index (PI), Bleeding on Probing (BOP), Periodontal Probing Depth (PPD), and changes in oral pathogen load assessed by quantitative PCR. The PTx800 group demonstrated a 100% reduction in BOP, achieving complete resolution of bleeding sites, compared to an 82% reduction in the active placebo group. PPD was stabilized in the PTx800 group and slightly worsened in the control group. Microbiological analysis revealed a significant reduction in the total bacterial load in the PTx800 group, with pronounced decreases in key red complex periodontal pathogens, including Porphyromonas gingivalis (Pg), Tannerella forsythia (Tf), and Treponema denticola (Td). PTx800 lozenges significantly improved clinical and microbiological measures of gingival health in older adults compared to active placebo. These findings suggest that PTx800 is a promising, non-antibiotic approach for managing oral inflammation and dysbiosis in aging populations, with potential implications for reducing oral pathogens strongly linked to systemic diseases.},
}

@article {pmid42991003,
year = {2026},
author = {Sharma, K and Bhushan, I and Sistla, S},
title = {Predictors of Psychological Stress and Infertility Among Reproductive-Age Women in Jammu and Kashmir: A Cross-Sectional Study.},
journal = {Health science reports},
volume = {9},
number = {11},
pages = {e73482},
pmid = {42991003},
issn = {2398-8835},
abstract = {BACKGROUND AND AIMS: Infertility affects nearly one in six individuals globally, with a substantial proportion of cases remaining idiopathic. Emerging evidence suggests that psychological stress may influence reproductive outcomes through neuroendocrine and immune pathways, potentially influencing the vaginal microbiome and the reproductive microenvironment. This study aimed to assess the prevalence of stress and infertility and examine their association among women of reproductive age in Jammu and Kashmir.

METHODS: A cross-sectional study was conducted among 1068 married women aged 18-48 years in Jammu and Kashmir, including women with idiopathic infertility and fertile controls. Data on sociodemographic characteristics, perceived stress, symptoms of reproductive tract infections (RTIs), sleep patterns, and physical stress manifestations were collected using a structured interviewer-administered questionnaire. Binary logistic regression analysis was performed to identify factors associated with psychological stress and infertility.

RESULTS: Overall, 37.6% of participants reported stress, while 29.3% had infertility. Stress was significantly associated with older age groups, employment status, lower financial status, RTI symptoms, physical stress manifestations, sleep duration, and infertility. Women with infertility had markedly higher odds of stress. Infertility was significantly associated with a history of stress, age, employment status, financial status, RTI symptoms, and sleep duration.

CONCLUSION: Psychological stress is strongly associated with infertility and related health and socioeconomic factors among women in this population. These findings highlight the potential interplay between psychological, reproductive, and social factors in reproductive health. Further longitudinal studies are needed to clarify causal pathways and inform targeted interventions.},
}

@article {pmid42991011,
year = {2026},
author = {Chen, L and Cheng, J and Mao, S},
title = {Mechanisms of resistance to immune checkpoint inhibitors in renal cell carcinoma and novel treatment strategies.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1984645},
pmid = {42991011},
issn = {2234-943X},
abstract = {In recent years, immune checkpoint inhibitors (ICIs), such as nivolumab, ipilimumab, pembrolizumab, and atezolizumab have substantially improved the prognosis of patients with advanced renal cell carcinoma. These agents have greatly changed the management of advanced renal cell carcinoma, shifting the treatment paradigm from cytokine and vascular endothelial growth factor-based therapies to immunotherapy strategies. However, drug resistance limits the long-term benefit. The mechanisms of immunotherapy resistance in RCC are complex. Recently, increasing research has focused on how cancer cells evade the surveillance and attack of the immune system and identifying the molecular and cellular drivers of resistance. In response, combination regimens incorporating ICIs are being developed to alleviate drug resistance and attack cancer cells through multiple pathways. At the same time, novel targeted strategies are under investigation to develop innovative approaches to delay, partially overcome, or bypass resistance in defined clinical settings. This review outlines the mechanisms of immunotherapy resistance in RCC from three interrelated perspectives: cancer cell-intrinsic mechanisms, the tumor microenvironment, and host related factors. We also summarize current efforts to overcome resistance, including ICI combined with tyrosine kinase inhibitors, dual ICI therapy, tumor microenvironment-targeting strategies, radiotherapy combined with immunotherapy, and gut microbiota modulation. Although these new strategies have shown different therapeutic effects in clinical trials, deeper understanding of immune regulation highlights their potential. Moreover, the integration of multi-omics analysis, and microbiome regulation may increase patient choices and optimize therapeutic outcomes, but their clinical efficacy has not been fully confirmed and requires prospective, treatment defined validation. Overall, ICIs have substantially changed RCC treatment, future progress will depend on deeper biological insights, rational combination design, and validated personalized immunotherapy.},
}

@article {pmid42991063,
year = {2026},
author = {Seri, A and Yue, B and Khawaja, M and Tang, WHW and Birnbaum, Y and Lavie, CJ and Virani, SS and Strauss, M and Krittanawong, C},
title = {Cardiovascular health and longevity: where are we?.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1921582},
pmid = {42991063},
issn = {2297-055X},
abstract = {Cardiovascular health is a key factor in human longevity, affecting not just lifespan but also the quality of aging. We synthesize evidence across four risk factor domains: genetic and epigenetic factors (APOE, FOXO3, telomere biology, epigenetic clocks); metabolic and vascular factors (hyperglycemia, dyslipidemia, obesity, arterial stiffness); lifestyle determinants (diet, physical activity, smoking, sleep, gut microbiome); and environmental exposure (air and noise pollution, climate stressors, ionizing radiation). These factors influence various biological processes such as oxidative stress, chronic low grade inflammation (inflammaging), mitochondrial dysfunction, metabolic disturbances, and changes in telomere length and epigenetics that collectively damage the endothelium, stiffen arteries, promote atherosclerosis, and contribute to overall cardiovascular decline with age. Understanding these processes helps explain why cardiovascular aging is such a strong predictor of mortality. We further summarize the principal intervention strategies with evidence for improving cardiovascular health and longevity, such as adherence to the American Heart Association's Life's Essential 8 construct, heart-healthy dietary patterns(Mediterranean, DASH), smoking cessation, sleep optimization, and reduction of environmental exposures. This narrative review distinguishes evidence derived from model organisms, human observational cohorts, and human interventional/genetic studies, since these evidence tiers differ substantially in their support for lifespan or longevity extending claims specifically, as opposed to cardiovascular risk reduction more broadly.},
}

@article {pmid42991095,
year = {2026},
author = {Mwesige, B and Angucia, B and Mbodi, L and Mwazha, A and Niyonzima, N and Mwansa-Kambafwile, J and Breiman, RF and Zakumumpa, H and Chikandiwa, A},
title = {The cervicovaginal microbiome as a candidate correlate and potential predictor of HPV clearance and treatment response after HSIL therapy: a scoping review.},
journal = {Frontiers in oncology},
volume = {16},
number = {},
pages = {1972845},
pmid = {42991095},
issn = {2234-943X},
abstract = {BACKGROUND: Persistent high-risk human papillomavirus (hrHPV) infection causes virtually all high-grade squamous intraepithelial lesions (HSIL) and cervical cancer, but only a minority progress, implicating host and microenvironmental cofactors. The cervicovaginal microbiome (CVM), particularly Lactobacillus-dominated communities, may influence hrHPV persistence, clearance, and response to HSIL treatment.

OBJECTIVE: To map evidence linking the CVM with hrHPV clearance and outcomes after HSIL treatment, including loop electrosurgical excision procedure (LEEP) and conization, using PRISMA-ScR and Arksey and O'Malley frameworks.

METHODS: Literature on cervicovaginal microbiota, community state types (CSTs), HPV natural history, HSIL/CIN treatment, probiotics, microbiome-directed interventions, and predictive biomarkers was systematically searched and narratively synthesized using a Population-Concept-Context framework.

RESULTS: Sixty-six sources were charted. Lactobacillus crispatus-dominated communities (CST-I) were associated with hrHPV clearance and favorable post-treatment outcomes, whereas CST-IV, bacterial vaginosis, and increased alpha-diversity were associated with hrHPV persistence, greater HSIL severity, and treatment failure. Proposed mechanisms include lactic acid-mediated pH regulation, D-lactic acid signaling, and modulation of viral oncoproteins and immune responses. Excision altered the CVM, with restoration of Lactobacillus dominance accompanying viral clearance. Microbial-signature machine-learning models showed promising but preliminary predictive performance. Oral and intravaginal probiotics showed inconsistent but generally favorable trends, with strongest evidence for intravaginal L. crispatus transplantation. Gut microbiome diversity may also influence chemoradiotherapy outcomes in invasive cervical cancer.

CONCLUSION: The CVM is a promising predictor of hrHPV clearance and HSIL treatment response. However, methodological heterogeneity, small cohorts, and limited prospective evidence restrict clinical translation. Large prospective studies and rigorously designed trials are needed to validate predictive signatures and determine whether microbiome profiling or targeted modulation can improve HSIL management and outcomes.},
}

@article {pmid42991189,
year = {2026},
author = {Chakravarthy, A},
title = {Cross-cohort generalization limitations in gut microbiome-based Alzheimer's disease classifiers: evidence from four supervised cohorts with batch-correction analysis.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1918251},
pmid = {42991189},
issn = {1663-4365},
abstract = {Gut microbiome dysbiosis has been proposed as an Alzheimer's disease (AD) biomarker, but the transportability of microbiome classifiers across independent cohorts remains uncertain. We reprocessed five public 16S rRNA cohorts (509 samples, China, Kazakhstan, South Korea) with a common DADA2/genus-level pipeline and evaluated logistic regression and LightGBM classifiers using nested within-cohort cross-validation, leave-one-cohort-out (LOCO) transfer, pairwise transfer, permutational multivariate analysis of variance (PERMANOVA), batch adjustment, and out-of-fold SHapley Additive exPlanations (SHAP) analyses. Within four labeled cohorts, using strict training-only genus selection as the primary classifier-performance pipeline (Section 2.5.1), within-cohort area under the receiver operating characteristic curve (AUC-ROC) ranged from 0.611 to 0.996. The near-perfect Li 2019 result was stable across 50 repeated nested-cross-validation (CV) partitions and exceeded a 1,000-permutation label null (p = 0.000999), though a technical metadata confound cannot be excluded (Section 4.3). In LOCO evaluation, AUC ranged from 0.506 to 0.812 (mean decreases of 0.170 for logistic regression and 0.133 for LightGBM); paired bootstrap intervals excluded zero for four of eight cohort-model differences. LOCO estimates agreed closely with a fixed common-universe reference retained for secondary analyses (max |Δ| = 0.066), though one pairwise-transfer cell changed materially (Kazakhstan→Ling 2020, LightGBM: 0.58 → 0.44), reported without smoothing. In the four-cohort marginal PERMANOVA model, cohort-associated compositional variation exceeded diagnosis-associated variation (R[2] = 0.172 vs. 0.014), decreasing to 0.059 vs. 0.023 when restricted to three more technically comparable Chinese paired-end MiSeq cohorts; dispersion differed significantly among cohorts. Label-blind transductive ComBat-seq and MMUPHin adjustment changed mean LOCO AUC by at most 0.007 and did not recover transferability. Cross-cohort overlap of top predictive taxa was low: logistic regression overlap remained above a prevalence-restricted null, while LightGBM did not. A descriptive coefficient-stability screen identified eight logistic-regression genera with opposite, stable fitted-coefficient directions across cohorts. These findings demonstrate substantial, heterogeneous cross-cohort generalization limitations among the evaluated public 16S datasets and show that, under the tested label-blind transductive design, the two batch-adjustment methods did not restore transferability. Prospective validation in larger, geographically and technically diverse cohorts is needed before microbiome-based AD classifiers can be considered clinically actionable.},
}

@article {pmid42991275,
year = {2026},
author = {Zhao, M and Mo, T and Huang, X and He, H and Long, F and Wu, P and Zou, Y},
title = {Integrated microbiome and metabolome analysis reveals mechanisms of Fusarium wilt resistance in banana rhizosphere soil under different continuous cropping durations.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1853743},
pmid = {42991275},
issn = {1664-302X},
abstract = {INTRODUCTION: Fusarium fungi are the primary causal agents of banana Fusarium wilt disease. In this study, using a resistant banana line (derived from cultivar Baodao), we observed that with increasing years of continuous cropping, the incidence of Fusarium wilt disease showed a notable reduction.

RESULTS: Microbial community abundance was lower in the susceptible banana variety (V) than in the resistant variety [sampled after one (S1), two (S2), and three (S3) years of continuous cropping]. With increasing continuous cropping years (S1, S2, and S3), microbial abundance increased, while the abundance of Fusarium oxysporum significantly decreased, and these changes coincided with visually healthier plant growth compared to the susceptible variety. However, the relative abundance of Fusarium, Bisifusarium Gibellulopsis, and Rectifusarium were the highest in V. Rozellomycota sp., Trichoderma virens, Trichoderma asperellum, and Hypocreaceae sp. were also identified with high abundance in S2 and S3, but were not detected in V. In addition, using Spearman's correlation analysis and network analysis (|r| > 0.6), we found that the reduction of Fusarium pathogens was significantly correlated with the enrichment of beneficial bacteria such as Sphingomonas parvus and Rozellomycota sp. A total of 1153 metabolites were identified, including amino acids, phenolic acids, organic acids, phenolic acids, and flavonols. Among these, 79 compounds showed a significant decrease in V but increased in S1, S2, and S3; these compounds were negatively correlated with Fusarium oxysporum and positively correlated with Rozellomycota sp. Additionally, 47 compounds were associated with Sphingomonas parvus, Bryobacter and other beneficial bacteria.

CONCLUSION: These findings suggest that specific metabolic compounds are associated with the enrichment of beneficial fungi and bacteria in the banana rhizosphere soil as continuous cropping time increases.},
}

@article {pmid42991397,
year = {2026},
author = {Li, M and Pang, L and Li, Y and Shang, S and Huang, C},
title = {Multi-omics profiling identifies a putative Akkermansia-HK3-lactate immunometabolic link associated with JPZS treatment in lupus nephritis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1873518},
pmid = {42991397},
issn = {1664-3224},
mesh = {Animals ; *Lupus Nephritis/drug therapy/metabolism/immunology ; Female ; Mice ; Multiomics ; *Hexokinase/metabolism/genetics ; Mice, Inbred MRL lpr ; *Akkermansia ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Gastrointestinal Microbiome/drug effects ; *Lactic Acid/metabolism ; Kidney/metabolism/pathology/drug effects ; Disease Models, Animal ; Mice, Inbred C57BL ; Metabolomics ; },
abstract = {BACKGROUND: Lupus nephritis (LN) is associated with aberrant glycolytic reprogramming in renal immune cells, yet its relationship with gut microbial alterations remains poorly defined. Hexokinase 3 (HK3) has emerged as a candidate metabolic node in myeloid activation, while the relationship between gut Akkermansia abundance and renal HK3-associated metabolic changes in LN remains unclear. We used Qihuang Jianpi Zishen decoction (JPZS), an herbal formula used as an adjunct in clinical practice, as an experimental probe to investigate this putative gut-immunometabolic connection through integrated multi-omics.

METHODS: Female MRL/lpr mice (n = 6 per group) received JPZS (6.305, 12.61, or 25.22 g/kg/day) or vehicle for 8 weeks, with C57BL/6 mice serving as a healthy reference group. Renal function, autoantibodies, histopathology, and glomerular IgG deposition were assessed across treatment groups. Integrated multi-omics profiling-fecal 16S rRNA sequencing, untargeted plasma metabolomics, and renal RNA sequencing-was performed in the matched control, model, and high-dose JPZS groups. Renal lactate and pyruvate were quantified, and HK3 and Ldhal6b mRNA and their corresponding proteins were evaluated by qPCR and western blotting. HK3/F4/80 dual immunofluorescence was additionally performed to examine the spatial localization of HK3 relative to renal macrophages.

RESULTS: JPZS reduced proteinuria, serum creatinine, glomerular IgG deposition, and renal histopathological injury in MRL/lpr mice. Gut microbiome profiling showed marked enrichment of Akkermansia and altered community composition, without significant recovery of Chao1 or Shannon diversity, accompanied by reductions in Klebsiella and Enterococcus. Plasma metabolomics revealed remodeling of amino-acid and central carbon metabolism, while renal transcriptomics identified immune-related differences and an exploratory glycolysis/gluconeogenesis enrichment signal. JPZS reduced renal lactate accumulation and the lactate/pyruvate ratio and decreased renal HK3 expression at both the mRNA and protein levels. Dual immunofluorescence showed increased HK3 and F4/80 fluorescence in model kidneys, with overlapping signals evident in merged images; both signals were lower following JPZS-H treatment. Cross-layer correlation analyses linked gut genera, circulating metabolites, and renal gene expression; targeted assays separately characterized renal lactate/pyruvate status.

CONCLUSION: JPZS ameliorated renal injury while inducing coordinated changes in the gut microbiome, circulating metabolome, and renal immunometabolic profile in MRL/lpr mice. Integrated multi-omics and targeted validation identified a putative Akkermansia-HK3-lactate immunometabolic link associated with JPZS treatment. These findings provide a hypothesis-generating framework for gut-kidney immunometabolic crosstalk in LN and warrant future causal validation through microbiota- and HK3-targeted approaches.},
}

Animals
*Lupus Nephritis/drug therapy/metabolism/immunology
Female
Mice
Multiomics
*Hexokinase/metabolism/genetics
Mice, Inbred MRL lpr
*Akkermansia
*Drugs, Chinese Herbal/pharmacology/therapeutic use
Gastrointestinal Microbiome/drug effects
*Lactic Acid/metabolism
Kidney/metabolism/pathology/drug effects
Disease Models, Animal
Mice, Inbred C57BL
Metabolomics

@article {pmid42991468,
year = {2026},
author = {Li, X and Liu, H and Wu, J and Xi, C},
title = {Distribution and resistance-associated genomic features of Acinetobacter in an urban wastewater network.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100673},
pmid = {42991468},
issn = {2666-5174},
abstract = {Acinetobacter spp. are important opportunistic pathogens with strong multidrug resistance potential, yet their distribution and associations with antibiotic resistance across urban wastewater systems remain poorly resolved. In this study, we characterized the spatiotemporal dynamics of Acinetobacter across an urban wastewater network including hospital, student residence hall, and wastewater treatment plant (WWTP) sites. A total of 300 wastewater samples were collected weekly over 1.5 years and analyzed by droplet digital PCR (ddPCR), with 94 samples further subjected to shotgun metagenomic sequencing. Acinetobacter was consistently detected across all sampling sites and ranked among the more abundant genera in site-pooled metagenomic community profiles. Throughout the WWTP treatment process, absolute Acinetobacter concentrations decreased by a median of 2.71 log10 units from influent to effluent, coinciding with a reduced ratio of Acinetobacter to total bacterial 16S rRNA gene copies. Cross-validated differential abundance analyses (DESeq2 and ANCOM-BC2) of the metagenomes corroborated this significant reduction in the effluent. Despite this removal efficacy, treated effluent maintained an average Acinetobacter concentration of 9.19 × 10[2] copies/100 mL, and the genus persisted as a highly abundant member of the effluent microbiome. Notably, Acinetobacter showed a positive association with 16S-normalized total antibiotic resistance gene (ARG) abundance (ρ = 0.570) that robust even remained significant after covariate adjustment (partial ρ = 0.508; 95% CI, 0.321-0.662). Genome-resolved analysis recovered 20 medium-to-high-quality Acinetobacter metagenome-assembled genomes, revealing site-specific lineage variations and identifying seven distinct OXA β-lactamase gene sequences. Although acquired ARG carriage and mobility were not established, the combined analyses support Acinetobacter as a widely detected genus associated with the wastewater resistome. From a public health perspective, tracking Acinetobacter alongside ARGs can characterize treatment-associated changes, provide bacterial-community context for resistance signals, and inform targeted genomic follow-up.},
}

@article {pmid42991495,
year = {2026},
author = {Buettner, C and Peterburs, P and Schulz-Kuhnt, A and Herrmann, L and Soeberdt, M and Abels, C},
title = {Peppermint oil exhibits antispasmodic and anti-inflammatory properties and alters gut microbial community composition and gas production in vitro.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1963380},
pmid = {42991495},
issn = {1663-9812},
abstract = {BACKGROUND: Peppermint oil (PMO) is an herbal medicinal product used for the symptomatic relief of minor spasms of the gastrointestinal tract, flatulence and abdominal pain, especially in patients with irritable bowel syndrome (IBS). To gain a more comprehensive understanding of the multimodal effects of PMO in IBS, the investigations aimed to confirm its antispasmodic and anti-inflammatory effects and assess direct effects of PMO on the human gut microbiome and microbial gas production in vitro.

METHODS: To investigate the spasmolytic activity of PMO (BNO 2910), circular smooth muscle strips from the proximal colon of five male guinea pigs were used. Its anti-inflammatory potential was evaluated using RAW 264.7 macrophages stimulated with LPS. TNF secretion and nitrite levels, as an indicator of NO production, were measured using ELISA and Griess reagent, respectively. Effects on the human gut microbiome and colonic fermentation activity were assessed in an anaerobic in vitro fermentation system inoculated with stool samples from six healthy donors using 16S rRNA gene sequencing, flow cytometry-based cell counting and gas production measurements.

RESULTS: PMO showed antispasmodic effects on isolated smooth muscle strips of guinea pig colon tissue as well as inhibition of LPS-induced TNF secretion and NO induction in RAW 264.7 macrophages. Additionally, PMO significantly reduced microbial gas production in stool samples from healthy donors, indicating reduced microbial fermentation activity under the experimental conditions, while the alpha diversity indices richness and evenness were maintained or even increased. At the genus level, PMO showed direct effects on microbiome community composition, inhibiting the growth of potential disease-related organisms (e.g., Escherichia-Shigella or Eggerthella), while maintaining or even increasing the abundance of health-related organisms (e.g., Blautia and Faecalibacterium).

CONCLUSION: Besides antispasmodic and anti-inflammatory effects, PMO exhibits direct effects on the human gut microbiome, including the modulation of microbial communities and total gas production in vitro. To determine the specific relevance of the observed microbiome-related effects of PMO in IBS further disease-specific studies are warranted.},
}

@article {pmid42991517,
year = {2026},
author = {Qi, Z and Wang, M and Li, Y and Tian, L and Liu, J},
title = {Molecular mechanisms by which the intratumoral microbiome drives pancreatic ductal adenocarcinoma progression and therapeutic response.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1970900},
pmid = {42991517},
issn = {1664-3224},
mesh = {Humans ; *Carcinoma, Pancreatic Ductal/microbiology/immunology/pathology/therapy/drug therapy ; *Pancreatic Neoplasms/microbiology/immunology/pathology/therapy/drug therapy ; Animals ; *Microbiota/immunology ; Disease Progression ; Tumor Microenvironment/immunology ; },
abstract = {Pancreatic ductal adenocarcinoma has an extremely poor prognosis. Pancreatic ductal adenocarcinoma harbors a multidomain intratumoral microbial community dominated by bacteria and also containing fungi; its composition differs fundamentally from that of normal pancreatic tissue and drives malignant progression through three major axes: inflammatory-immune signaling, metabolic-epigenetic regulation, and stromal remodeling. Gammaproteobacterial lipopolysaccharide establishes a chronic proinflammatory microenvironment through the Toll-like receptor 4-nuclear factor kappa B axis, whereas in situ gemcitabine inactivation by the long isoform of bacterial cytidine deaminase represents the best-supported microbiome-mediated mechanism of drug resistance to date. In experimental systems, Fusobacterium nucleatum has been linked to tumor-cell invasion and alternatively activated macrophage polarization. In mouse and cell models, intratumoral fungi have been implicated in immunosuppressive signaling through the C-type lectin receptor dectin-1-interleukin 33 axis and the mannose-binding lectin-complement pathway; their relevance to human pancreatic ductal adenocarcinoma remains debated. These three axes may converge on stromal activation and epithelial-mesenchymal transition and contribute to invasion and treatment resistance. Antimicrobial strategies targeting drug-resistance-associated bacteria can restore gemcitabine efficacy in animal experiments and have been explored experimentally alongside programmed cell death protein 1 blockade; the clinically appropriate patient populations and optimal sequencing of such combinations remain to be defined in prospective trials.},
}

Humans
*Carcinoma, Pancreatic Ductal/microbiology/immunology/pathology/therapy/drug therapy
*Pancreatic Neoplasms/microbiology/immunology/pathology/therapy/drug therapy
Animals
*Microbiota/immunology
Disease Progression
Tumor Microenvironment/immunology

@article {pmid42991545,
year = {2026},
author = {Saeed, U and Piracha, ZZ},
title = {Phage-directed precision microbiome medicine: engineering pathobiont depletion, synbiotic succession, microbial-function editing, metabolite host signaling, neurophagomics, and durable ecological state control in gut dysbiosis associated diseases.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1964616},
pmid = {42991545},
issn = {1664-302X},
abstract = {Bacteriophages are being investigated as strain-selective tools for modifying intestinal microbial communities, but the evidence supporting ecological reconstruction is substantially less mature than the evidence supporting targeted bacterial depletion. This review separates current knowledge into three domains: established and emerging experimental evidence, human translational evidence, and hypotheses proposed for future testing. Human studies show that orally administered natural or engineered phages can be recovered from the gastrointestinal tract and can alter selected bacterial populations without antibiotic-like loss of overall community diversity. Preclinical studies further demonstrate targeted suppression of inflammatory Klebsiella pneumoniae in inflammatory bowel disease models, cytolytic Enterococcus faecalis in alcohol-associated liver disease, evolutionary steering of Escherichia coli, in situ bacterial genome editing, local therapeutic-protein production, and phage-probiotic cooperation. These findings do not yet establish that an integrated phage-successor-prebiotic sequence can durably reprogram a human gut ecosystem. To organize this translational gap, we use Subtract-Seed-Feed-Lock as an explicitly proposed design framework. A phage or phage-derived platform first depletes, weakens, or edits a disease-relevant bacterial strain or function; a niche-matched successor is then introduced; a selectively utilized nutrient supports that successor; and durability is assessed after treatment withdrawal. Related terms used in this review-Functional Phageability, Minimum Ecological Dose, Ecological Vacancy Window, nutrient-conditioned phagogram, ecological pharmacokinetics/pharmacodynamics (Eco-PK/PD), ecological pharmacovigilance, neurophagomic reverse translation, and microbiome-state digital twin-are hypothesis-generating operational concepts rather than validated clinical methods. Host signaling is likewise framed as predominantly indirect: phage-induced changes in bacterial abundance or function may alter lipopolysaccharide, short-chain fatty acids, indoles, bile acids, and other metabolites that subsequently engage inflammatory, barrier, hepatic, or neural pathways. The gut-brain application remains especially preliminary; targeting urdA-positive imidazole-propionate producers has not been validated with therapeutic phages. Clinical development will require reproducible good manufacturing practice, control of endotoxin and host-cell contaminants, product stability, resistance and immune-neutralization monitoring, environmental-shedding assessment, and regulatory strategies for genetically modified, dynamically updated, and multi-component products. The immediate opportunity is therefore precise microbial perturbation with evidence-matched endpoints; durable programmed reconstruction remains an experimentally testable objective.},
}

@article {pmid42991559,
year = {2026},
author = {Wu, J and Jiang, T and Li, X and Xie, D and Xie, K},
title = {Bidirectional relationship between diabetes and pancreatic cancer: from mechanistic investigation to clinical application.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {1995824},
pmid = {42991559},
issn = {1664-2392},
mesh = {Humans ; *Pancreatic Neoplasms/pathology/metabolism/complications/etiology ; *Diabetes Mellitus, Type 2/complications/metabolism/pathology ; *Carcinoma, Pancreatic Ductal/pathology/metabolism ; Animals ; },
abstract = {A well-established bidirectional causal relationship connects type 2 diabetes mellitus (T2DM) and pancreatic ductal adenocarcinoma (PDAC). Long-standing T2DM elevates pancreatic cancer risk approximately 1.8-2.2-fold, whereas 30%-74% of PDAC patients develop new-onset diabetes (NOD) 2-36 months before tumor detection, which mostly corresponds to tumour-originated type 3c pancreatogenic diabetes (T3cDM). Notably, 25%-40% of such patients achieve spontaneous glycemic recovery after R0 curative resection, solidifying the causal nature of PDAC-induced hyperglycemia. Six interrelated molecular mechanisms mediate their reciprocal crosstalk: chronic metabolic abnormality mediated by hyperinsulinemia and AGE-RAGE signaling, sustained inflammatory and macrophage remodeling, KRAS-driven oncogenic and epigenetic modification, pancreatic stellate cell-derived desmoplasia, tumor exosome-mediated β-cell damage, and gut-pancreas microbiome dysbiosis. Specifically, PDAC-secreted exosomes loaded with adrenomedullin, peritumor fibrotic islet destruction and circulating S100A8 peptide collectively lead to insulin deficiency, making T3cDM biochemically distinguishable from insulin-resistant classic T2DM by reduced pancreatic polypeptide and endogenous insulin concentrations. Clinically, END-PAC scoring and emerging machine learning algorithms facilitate risk stratification for early PDAC screening among patients aged 50 years or older with NOD. Nonetheless, prominent challenges remain: conflicting clinical data on the anti-PDAC potential of metformin and GLP-1RAs, ethnic heterogeneity limiting the generalizability of current prediction models, and up to 88% T3cDM misdiagnosis owing to the absence of global unified diagnostic benchmarks. Future translational research will center on prospective validation of multi-omic biomarkers, formulation of standardized T3cDM diagnostic criteria, large-scale screening trials, and rational repurposing of antidiabetic agents for pancreatic cancer prevention and adjuvant therapy.},
}

Humans
*Pancreatic Neoplasms/pathology/metabolism/complications/etiology
*Diabetes Mellitus, Type 2/complications/metabolism/pathology
*Carcinoma, Pancreatic Ductal/pathology/metabolism
Animals

@article {pmid42991579,
year = {2026},
author = {Yan, H},
title = {From biomarker discovery to prediction models: clinical translation of multi-omics for early prediction of gestational diabetes mellitus.},
journal = {Frontiers in endocrinology},
volume = {17},
number = {},
pages = {2007266},
pmid = {42991579},
issn = {1664-2392},
mesh = {Humans ; *Diabetes, Gestational/diagnosis/metabolism ; Pregnancy ; Female ; *Biomarkers/analysis/metabolism ; Multiomics ; Translational Research, Biomedical ; Metabolomics/methods ; Prognosis ; },
abstract = {Gestational diabetes mellitus (GDM) affects roughly one in seven pregnancies worldwide, yet diagnosis by oral glucose tolerance testing at 24-28 weeks of gestation leaves only a narrow window for intervention. The demonstrated benefit of treating early-diagnosed GDM has intensified interest in first-trimester prediction. This narrative review synthesises recent advances in early-pregnancy biomarkers for GDM, shifting the emphasis from biomarker discovery to clinical translation. Conventional lipid indicators and composite indices provide moderate predictive power at minimal cost (odds ratios 1.4-1.7; AUCs 0.75-0.82). Metabolomic and lipidomic studies have identified recurrent signatures - phospholipid remodelling, glycerolipid accumulation, fatty acid and acylcarnitine excess, branched-chain amino acids and bile acids - that map onto insulin resistance, lipotoxicity and hepatic steatosis, and omics-enhanced models report derivation-stage AUCs of approximately 0.83-0.95 with apparent incremental value over clinical factors alone, although these estimates derive predominantly from small cohorts that have rarely undergone external validation. Gut-microbiome features, thyroid parameters and environmental exposures further widen the aetiological frame. Translation remains limited, however, by small derivation cohorts, scarce external validation, analytical heterogeneity and the absence of trials testing biomarker-guided early intervention. We propose a pragmatic roadmap towards clinically deployable first-trimester prediction, with particular attention to high-burden Asian populations.},
}

Humans
*Diabetes, Gestational/diagnosis/metabolism
Pregnancy
Female
*Biomarkers/analysis/metabolism
Multiomics
Translational Research, Biomedical
Metabolomics/methods
Prognosis

@article {pmid42991605,
year = {2026},
author = {Hauser, W and Keller, JE and Pasnoor, M and Wright, DE},
title = {Small-fiber degeneration, sensory dysfunction, and nociception comorbidity in central neurodegenerative disease.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1854989},
pmid = {42991605},
issn = {1663-4365},
abstract = {Progressive neurodegenerative disease typically calls for clinical effort to improve cognitive and motor deficits. It is also focused on improving patients' quality of life. However, across these dementias and other diseases, the underlying causes and potential mechanisms remain unclear. Most experimental and clinical research focuses on the central nervous system, examining pathogenic proteins such as tau and amyloid beta, as well as the potential cascade following mitochondrial damage and neuroinflammation. Although peripheral involvement, including gut microbiome influences and other visceral organs, is well-documented, the peripheral nervous system remains an understudied component of these progressive diseases. As peripheral terminals of primary afferent neurons are exposed to inflammatory or toxic mediators, these neurons respond to these threats via neuron-specific phenotypic changes, including the generation of pain. Although normal peripheral sensitization is protective, exposure to damage in a chronic disease state can have long-term detrimental effects. Diseases that lead to central neurodegeneration often also feature peripheral neuropathy and chronic pain. We provide an overview of the incidence of peripheral neuropathy within these diseases, the contribution of changes in sensation to disease, and secondary neuropathic phenotypes resulting from disease. Woven in are discussions of the intersection of degeneration and toxic protein aggregation, briefly touching on resulting inflammatory signaling. Altogether, this review aims to synthesize current understanding of sensory peripheral nerve involvement across these neurodegenerative diseases.},
}

@article {pmid42991656,
year = {2026},
author = {Yoon, EJ and Ha, N and Jeong, MC},
title = {Spectrum-dependent dysbiosis and recovery patterns of the gut microbiota following antimicrobial exposure.},
journal = {iScience},
volume = {29},
number = {11},
pages = {118069},
pmid = {42991656},
issn = {2589-0042},
abstract = {Broad-spectrum antimicrobials profoundly alter gut microbial ecosystems; however, post-antimicrobial recovery remains incompletely understood. Here, we used a short-term oral exposure model in mice treated with clindamycin, moxifloxacin, or ceftriaxone, representing antimicrobials with distinct antibacterial spectra. Each antimicrobial induced distinct patterns of gut microbiota perturbation and cecal enlargement. At day 0, immediately after antimicrobial exposure, antimicrobial-specific differences in microbial composition and diversity were observed, followed by distinct recovery trajectories through days 3 and 5. Clindamycin induced sustained dysbiosis with limited recovery, whereas ceftriaxone caused pronounced initial disruption followed by partial recovery by day 5. Moxifloxacin produced transient perturbation with greater recovery of microbial diversity. Together, analyses of taxonomic composition, α-diversity, and β-diversity demonstrated that both the magnitude of the initial perturbation and early recovery were antimicrobial dependent. These findings delineate spectrum-dependent patterns of gut microbiota disruption and early recovery following antimicrobial exposure and highlight antimicrobial-specific effects on gut microbial resilience.},
}

@article {pmid42991692,
year = {2026},
author = {Mason, CJ and Hansen, TE and Newell, N and Corpuz, RL and Geib, SM},
title = {Full-length 16S rRNA gene sequencing resolution reveals variable compositional features of medfly gut microbiomes.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag292},
pmid = {42991692},
issn = {2730-6151},
abstract = {Insects have interconnected relationships with gut microorganisms that can have impacts on behavior and survival. Understanding the foundational ecological principles of insect-associated microorganisms can reveal how insects utilize microbes to cope under challenging conditions. Surveys of insect microbiomes often utilize 16S rRNA gene (16S) sequencing of metagenomic DNA, with target amplicon regions and lengths typically selected based on the limitations of short-read sequencing technology read lengths. Targeting partial 16S amplicons may obfuscate ecological signal, and methods which are agnostic to amplicon length allow targeting of the entire 16S gene and may aid in overcoming this hurdle. In this study, we illustrate the advantage of full-length 16S sequencing utilizing PacBio HiFi sequencing in comparison to V4, which provides new insight into the gut microbiome community composition of an invasive insect. We evaluated the gut microbiome of mass-reared medfly males (Mediterranean fruit fly, Ceratitis capitata) that were collected across a 9-month sampling period. Full-length 16S PCR products were prepared into a Kinnex 16S library, sequenced on a PacBio Revio system, and the resulting HiFi sequences were processed into amplicon sequence variants (ASVs). Substantial differences in bacterial ASV compositions were observed across medfly cohorts using full-length amplicons, which were subdued using V4 regions. Species-level gut microbiome variation were supported with genomes assembled from shotgun metagenomic sequencing. Our results highlight how highly accurate long-read sequencing of full-length 16S amplicons can uncover ecological interactions between host and gut microbiomes and serve as a bridge between short-fragment amplicons and shotgun metagenomics.},
}

@article {pmid42991758,
year = {2026},
author = {van Eijnatten, AL and Vultaggio, G and Schram, M and Cajas Muñoz, D and Guandalin Zagatto, LF and Morriën, E and Bodelier, PLE and Snoek, BL and Lejoly, J and van der Putten, WH and Veen, GFC},
title = {Towards personalized and lifestyle-inspired soil management: lessons from the gut microbiome.},
journal = {Npj soil ecology},
volume = {1},
number = {1},
pages = {5},
pmid = {42991758},
issn = {3091-2814},
abstract = {Soil microorganisms are key drivers of ecosystem functions supporting biodiversity, food production, and climate regulation. Restoring multiple ecosystem functions under intensive land-use and climate change requires steering microbiome composition. However, this remains challenging due to the high complexity of soils and the assembly rules of their microbiomes. As the extensively studied human gut microbiome has considerable similarities with the soil microbiome, we explore advances in steering the human gut microbiome composition to improve the steering of soil microbiomes.},
}

@article {pmid42991825,
year = {2026},
author = {Iuga, MM and Ramírez-Mora, T and Oprea, B and Espada-Salgado, FM},
title = {DNA extraction methods and pre-analytical workflows for next-generation sequencing in infected dental pulp and endodontic infections: A scoping review.},
journal = {Journal of clinical and experimental dentistry},
volume = {18},
number = {10},
pages = {e1181-e1197},
pmid = {42991825},
issn = {1989-5488},
abstract = {BACKGROUND: Next-generation sequencing (NGS) has improved the characterization of microbial communities in infected dental pulp and endodontic infections. However, variability in sampling procedures, DNA extraction methods, contamination control, and quality assessment may affect microbial recovery and limit comparability across studies. This scoping review mapped the available evidence on DNA extraction methods and pre-analytical workflows used for NGS in human infected dental pulp and endodontic infections.

MATERIALS AND METHODS: This scoping review was conducted according to Joanna Briggs Institute guidance and reported following PRISMA-ScR. Searches were performed in Scopus, Web of Science Core Collection, Embase, PubMed/MEDLINE, and LILACS, with additional screening of Google Scholar and ClinicalTrials.gov, from 2011 to March 23, 2026. Records were deduplicated in Zotero and screened in Rayyan by two independent reviewers, with disagreements resolved by discussion or a third reviewer. Data were descriptively charted for specimen type, sampling procedures, storage, contamination control, lysis and extraction methods, sequencing platforms, bioinformatic processing, and quality metrics.

RESULTS: Of 389 records identified, 219 remained after duplicate removal, 44 full-text articles were assessed, and 30 studies were included. Most studies used short-read 16S amplicon sequencing, mainly on Illumina platforms. Specimens included paper-point samples, endodontic files, pulp tissue, cryopulverized root segments, root apices, and periapical lesions. Substantial heterogeneity was observed in lysis strategies, extraction kits, matrix processing, contamination controls, and pre-sequencing quality assessment.

CONCLUSIONS: Pre-analytical heterogeneity limits reproducibility and cross-study comparability in endodontic NGS research. Standardized reporting, matrix-specific DNA extraction validation, systematic contamination controls, and transparent quality metrics are needed to strengthen future endodontic microbiome studies.},
}

@article {pmid42991842,
year = {2026},
author = {Mi, Y and Sun, P and Hao, Q and Yang, Y and Dong, C and Kong, C and Li, L and Zhao, C and Yin, H},
title = {Altered gut microbiota and untargeted metabolomic features in patients with schizophrenia: a case-control study.},
journal = {Frontiers in psychiatry},
volume = {17},
number = {},
pages = {1981601},
pmid = {42991842},
issn = {1664-0640},
abstract = {BACKGROUND: Mental disorders are among the leading causes of global disease burden, and their etiology spans genetic, environmental, and physiological factors. Emerging evidence suggests that the gut microbiota may contribute to the development of neuropsychiatric disorders through the microbiota-gut-brain axis. This study aimed to characterize differences in gut microbial composition and untargeted metabolomic profiles between patients with schizophrenia and healthy controls.

METHODS: Fecal samples were collected from 30 patients with schizophrenia and 30 healthy controls; 59 samples (30 patients and 29 controls) yielded qualified 16S rRNA gene sequencing data. Untargeted metabolomic profiling was performed by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS).

RESULTS: Compared with healthy controls, patients with schizophrenia showed reduced microbial richness and diversity together with marked separation in β-diversity. In an exploratory random forest ranking, Pseudocitrobacter, Hafnia-Obesumbacterium, and Escherichia-Shigella contributed most strongly to between-group discrimination. Escherichia-Shigella was significantly enriched in patients (median relative abundance 2.377% in group S vs. 0.119% in group H; q = 0.00031; Cliff's δ = 0.646), whereas Faecalibacterium (2.630% vs. 7.275%) and Agathobacter (0.903% vs. 2.874%) were more abundant in healthy controls. Untargeted metabolomics likewise revealed between-group differences that predominantly involved metabolites and pathways of amino acid and lipid metabolism.

CONCLUSION: Patients with schizophrenia show alterations in gut microbial composition and untargeted metabolomic features, supporting an association between schizophrenia and microbiota-metabolite alterations. Future confirmation requires larger longitudinal cohorts and independent validation datasets. Owing to the small sample size, cross-sectional study design, and antipsychotic drug exposure, we could not disentangle disease-specific effects from medication-related effects.},
}

@article {pmid42992114,
year = {2026},
author = {Castro E Silva, M and Silva, E and Nunes, C and Baldaia, L and Orelhas, L and Costa, J and Dias, P and Tavares, B and Fonseca, M},
title = {The gut microbiome and vascular disease - A systematic review of mechanistic insights and implications for vascular surgery.},
journal = {JVS-vascular science},
volume = {7},
number = {},
pages = {100454},
pmid = {42992114},
issn = {2666-3503},
abstract = {OBJECTIVE: Observational studies repeatedly linked gut microbial features and metabolites to vascular disease, but it is unclear which associations are reproducible, which remain significant after confounder adjustment, and how they relate to experimental evidence. This review aims to determine which taxa and metabolites are consistently associated across independent human studies; whether the population, phenotype, method, and sample type explain divergent findings; and where the human data converge with, diverge from, or remain untested with the animal and interventional literature.

METHODS: PubMed/MEDLINE, Embase, Web of Science, and Cochrane Library were searched for human studies of the gut microbiome composition or gut-derived metabolites reporting atherosclerotic, aneurysmal, peripheral arterial, calcific, or arterial stiffness outcomes from database inception to December 31, 2025. Study screening and duplicate article extraction were conducted following the Preferred Reporting Items for Systematic reviews and Meta-Analyses 2020 guidelines. The study design was classified explicitly, the covariates in each primary analysis were extracted, and the risk of bias was assessed using the Newcastle-Ottawa Scale or the Joanna Briggs Institute checklist. The findings were then compared with the animal and human interventional literature identified through targeted searching.

RESULTS: All the 29 included reports were observational (19 cross-sectional, 3 case-control, and 7 cohort) studies, and none was interventional. The reproducible findings were the enrichment of Proteobacteria-affiliated genera (5 reports) and of oral-origin organisms (3 reports), and the depletion of butyrate producers in carotid disease. The carnitine pathway intermediates gamma-butyrobetaine and trimethyllysine were independently associated with cardiovascular death and major adverse limb events (hazard ratio, 1.93; 95% confidence interval, 1.35-2.76) in two independent cohorts. Trimethylamine N-oxide (TMAO) was outcome-specific; TMAO levels were associated with 5-year mortality in peripheral arterial disease (adjusted hazard ratio, 2.06; 95% confidence interval, 1.36-3.11) and with ankle-brachial-index-defined disease in diabetes (odds ratio, 1.051), but TMAO levels were lower in large-artery stroke than in controls and were unrelated to carotid or limb outcomes once renal function was modelled. In addition, 16 of 29 reports fitted a multivariable model, and only three included renal function; the compositional findings were almost exclusively unadjusted. The risk of bias was good in 11 reports, moderate in 16, and low in 2. Animal models causally implicate TMAO in atherogenesis and aneurysm formation and show butyrate and Roseburia intestinalis to be protective, but the results of germ-free experiments and the only human fecal transplantation trial are discordant.

CONCLUSIONS: A small number of gut microbial signals are reproducible, but most have not been adjusted for potential confounders, particularly renal function, which may partly explain the observed associations. The carnitine pathway metabolites with the strongest prognostic signal in surgical populations have never been tested in an animal vascular model. Microbiome profiling has no current role in vascular surgical practice.},
}

@article {pmid42992150,
year = {2026},
author = {Nannini, K and Krutkin, DD and Kelley, ST and Ortiz-Velez, A and Brown, JD and Ogden, S and Terrazas, F and Barber, NA},
title = {Moisture and material shape microbial communities in the built environment through disturbance-productivity relationships.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21859},
pmid = {42992150},
issn = {2167-8359},
mesh = {*Fungi/classification/genetics/isolation & purification ; *Construction Materials/microbiology ; *Built Environment ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; Biodiversity ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: The built environment houses diverse microbial communities whose diversity and composition differ among building materials and environmental conditions. Ecological theory makes predictions about how productivity and diversity shape communities, and experiments in the built environment provide an opportunity to test these predictions. We manipulated moisture (constant or repeated wet-dry cycling) on three common building materials to test hypotheses that environmental disturbance interacts with the potential productivity of building materials to influence alpha and beta diversity.

METHODS: Coupons of different building materials, medium density fiberboard, gypsum wallboard and oriented strand board, were sterilized before passive inoculation, then kept wet or periodically air-dried before rewetting. Microbial communities were sampled using swabs every 14 days for 7-week period. Productivity was measured using bacterial cell counts, fungal hyphal length, and fungal spore density, and microbial diversity was determined via community amplicon sequencing using universal bacterial (16S) and fungal (ITS) primers.

RESULTS: The most productive material (oriented strand board) supported the highest bacterial alpha and beta diversity, and these diversity levels were reduced by repeated drying disturbances. Diversity patterns for fungi were more variable, with the highest alpha diversity on low-moderate productivity material (gypsum wallboard). Fungal beta diversity was reduced by disturbance on high productivity material but increased on the other materials. These patterns were driven largely by members of Bacillaceae, Sphingomonadaceae, and Aspergillaceae that reached high abundances in some treatments.

CONCLUSIONS: Disturbance regime interacted with building material, so disturbance effects depended on material type. There were also differences between bacteria and fungi, which may be due to the scale-dependence of productivity-diversity relationships, but this pattern was not uniform. Network analysis found evidence of multi-species complexes of bacteria and fungi known to form biofilms, as well as evidence of competitive exclusion on specific materials and conditions. Together, these results indicate that disturbances can interact with building materials, and that these disturbances may be strongly mediated by biotic interactions.},
}

*Fungi/classification/genetics/isolation & purification
*Construction Materials/microbiology
*Built Environment
*Bacteria/classification/genetics/isolation & purification
*Microbiota
Biodiversity
RNA, Ribosomal, 16S/genetics

@article {pmid42992162,
year = {2026},
author = {Tosefsky, K and Schaffner, SL and Lam, JST and Wang, YN and Keymanesh, S and Kuan, AJ and Metcalfe-Roach, A and Cirstea, MS and Sacheli, MA and Morelli, TF and Yap, M and Brigden, O and Gill, M and Cohen, TR and Stukas, S and Finlay, BB and Appel-Cresswell, S},
title = {Mediterranean-ketogenic vs. medium-chain triglyceride supplemented Mediterranean diet: Effects on the gut-brain-immune axis in Parkinson's disease.},
journal = {iScience},
volume = {29},
number = {11},
pages = {117981},
pmid = {42992162},
issn = {2589-0042},
abstract = {Ketogenic diets have been proposed as potential neuroprotective interventions for Parkinson's disease (PD), but concerns remain regarding their effects on the gut microbiome and gut-brain-immune axis. We conducted a randomized crossover trial comparing 8-week Mediterranean-ketogenic (MeDi-KD) versus medium-chain triglyceride-supplemented Mediterranean (MeDi-MCT) diets, separated by an 8-week washout (NCT05469997). Primary outcomes included changes in gut microbiome taxonomic and functional profiles, fecal short-chain fatty acid (SCFA) production, and biomarkers of intestinal permeability and inflammation. Neither intervention significantly altered microbiome diversity or functional gene abundance, established features of PD-associated dysbiosis, nor fecal or plasma biomarkers of intestinal permeability (zonulin) or inflammation (calprotectin). The MeDi-KD modestly reduced total fecal SCFAs, while both interventions increased the relative abundance of Roseburia hominis, and the MeDi-MCT was associated with decreases in plasma IL-1β and IL-8. No severe adverse events were reported, supporting further investigation of MeDi-KD strategies in larger, longer-duration PD trials.},
}

@article {pmid42992351,
year = {2026},
author = {Wang, Y and Han, S and Liu, X and Dang, H and Zheng, C and Zheng, Y and Cao, C and Wu, Y},
title = {Long-term salinity is associated with deteriorated soil properties, rhizosphere microbiome restructuring, and elevated wheat crown rot: evidence from a 19-year gradient experiment and a 3-year remediation verification.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1992882},
pmid = {42992351},
issn = {1664-462X},
abstract = {Soil salinization threatens global agricultural sustainability and may elevate soil-borne disease risk through coordinated changes in soil conditions and the rhizosphere microbiome, yet long-term field evidence remains limited. Here, a 19-year controlled field experiment with an artificial salinity gradient (non-saline, moderate, and severe) was conducted to characterise salinity-associated responses of soil physicochemical properties, wheat crown rot (WCR), and the rhizosphere microbiome. A 3-year field remediation demonstration was implemented to test whether replacing saline irrigation with non-saline water could reverse soil deterioration and reduce disease severity. The results showed that severe salinity increased soil pH from 7.64 to 8.38 and reduced available phosphorus, total nitrogen, and available potassium by 54.11%, 14.63%, and 37.69%, respectively, while the WCR disease index increased from 10.51 to 32.88. It also reduced microbial richness and diversity, altered rhizosphere community composition, with taxon-specific abundance shifts among halophilic taxa, and redistributed community functional potential, with greater representation of genes associated with compatible-solute metabolism and ion homeostasis alongside changes in carbon, nitrogen, and sulfur metabolism. Remediation reduced soil salinity and pH, improved nutrient availability, and decreased the WCR disease index by 49.17%. Together, our results show that long-term salinization is associated with coordinated deterioration of soil conditions, restructuring of the rhizosphere microbiome, redistribution of microbial functional potential, and increased WCR severity. The remediation experiment showed that reducing salinity improved soil conditions and reduced disease severity. Re-establishing favourable soil abiotic conditions may be a prerequisite for alleviating disease risk in salinized agroecosystems.},
}

@article {pmid42992414,
year = {2026},
author = {Zhao, J and Su, Q and Wang, S and Liao, X and Li, Q and Chen, L and Kang, X and Xu, Q and Wu, Y and Liu, C and Zhao, H},
title = {Bacterial community response to postmortem changes predicts the causes of death and postmortem interval.},
journal = {Medicine, science, and the law},
volume = {},
number = {},
pages = {258024261505250},
doi = {10.1177/00258024261505250},
pmid = {42992414},
issn = {2042-1818},
abstract = {Determining the postmortem interval (PMI) and cause of death (COD) in decomposed remains a major challenge in forensic pathology because morphological and biochemical indicators progressively deteriorate during decomposition. Microbial communities are highly responsive to environmental and physiological changes and may therefore provide complementary forensic information. In this study, we used a murine model to investigate postmortem microbial succession associated with three death-related conditions-ligature strangulation (LS), hemorrhagic shock (HS), and organophosphate poisoning (OP)-across postmortem time points from 2 to 20 days. Swab samples from three skin sites (face, chest, and abdomen) were collected and subjected to 16S rDNA sequencing, and microbial community dynamics were evaluated using bioinformatics and random forest (RF) machine-learning models. Our results revealed distinct COD-associated microbial trajectories. LS carcasses exhibited accelerated morphological decomposition and earlier Proteobacteria dominance, whereas HS showed delayed decomposition-related changes. OP exhibited distinct microbial diversity and succession patterns, particularly during early PMI. Alpha- and beta-diversity analyses indicated that both COD and PMI significantly influenced microbial community structure. RF models showed strong discriminatory performance for COD classification (AUC > 0.95) and PMI classification (AUC 0.88-0.98), with distinct microbial features contributing to the two classification tasks. These findings suggest that physiological conditions associated with different causes of death may contribute to distinct postmortem microbial trajectories, while temporal microbial succession provides informative markers for categorical PMI classification. Collectively, microbiome-based approaches may serve as complementary forensic tools for simultaneous PMI classification and discrimination of death-related conditions.},
}

@article {pmid42992548,
year = {2027},
author = {Zhu, LX and Jiang, GJ and Gao, FH and Du, YQ},
title = {Metabolic reprogramming of myeloid‑derived suppressor cells in colorectal cancer: Mechanistic insights and immunometabolic targeted rehabilitation (Review).},
journal = {Molecular medicine reports},
volume = {35},
number = {1},
pages = {},
doi = {10.3892/mmr.2026.14061},
pmid = {42992548},
issn = {1791-3004},
mesh = {*Myeloid-Derived Suppressor Cells/metabolism/immunology ; Humans ; *Colorectal Neoplasms/metabolism/immunology/therapy/pathology ; *Metabolic Reprogramming ; Animals ; Immunotherapy/methods ; Tumor Microenvironment/immunology ; },
abstract = {Metabolic reprogramming of myeloid‑derived suppressor cells (MDSCs) plays a role in immunotherapy resistance in colorectal cancer (CRC). This metabolic reprogramming appears to be coordinated by oncogenic mutations (such as adenomatous polyposis coli, KRAS and TP53) through a proposed self‑reinforcing 'mutation‑metabolism‑suppression' axis. In the present review, four core metabolic pillars sustaining MDSC pathogenicity and the epimetabolic regulation that durably locks them into a suppressive state were examined. Furthermore, two emerging dimensions were highlighted: The spatial metabolic antagonism through which MDSCs may construct a metabolically hostile zone to limit the functional activity of tertiary lymphoid structures, and the remote manipulation of MDSC function by gut and intratumoral microbiota‑derived metabolites. To transcend the limitations of non‑specific myeloid depletion, immunometabolic rehabilitation is proposed as a potentially transformative framework targeting intrinsic metabolic vulnerabilities to functionally reprogram MDSCs from an immunosuppressive to a homeostatic or immunostimulatory phenotype. By integrating emerging spatial omics for precise target validation, artificial intelligence‑guided rational drug design and microbiome modulation, this paradigm provides a strategic roadmap for next‑generation precision immunotherapy, aiming to achieve durable responses across both microsatellite stable and microsatellite instability‑high CRC.},
}

*Myeloid-Derived Suppressor Cells/metabolism/immunology
Humans
*Colorectal Neoplasms/metabolism/immunology/therapy/pathology
*Metabolic Reprogramming
Animals
Immunotherapy/methods
Tumor Microenvironment/immunology

@article {pmid42992593,
year = {2026},
author = {Kramer, ML and Ho, AK and Lamprecht, E and Bradbury, M and Kramer, CM and Finlay, KA},
title = {The Health Influencer-Interactor Framework: Enhancing participant retention in health research through strategic marketing integration.},
journal = {Health marketing quarterly},
volume = {},
number = {},
pages = {1-19},
doi = {10.1080/07359683.2026.2758042},
pmid = {42992593},
issn = {1545-0864},
abstract = {Health research participation attrition limits research success, resulting in revenue losses, sample bias, and an inability to accurately generalize results. A systematic framework is needed to enable health marketers to combine psychosocial motivators from citizen science and online influencer marketing to drive sustained research participation. The Health Influencer-Interactor Framework (HIIF) is a theoretically-based architecture that integrates these motivators into recruitment strategy, communication messaging and online influence to attain higher research retention rates. This paper presents the underpinning foundations of the HIIF and illustrates its application through a urinary microbiome research case study. Participants recruited via influencer channels (21.51% retention, N = 188) exhibited higher retention rates than non-influencer-recruited participants (11.01% retention, N = 127). The HIIF addresses the growing need for social influence-based digital solutions in health research marketing, offering a theoretically-informed approach that substantially contributes to more efficient clinical trials and health studies. Findings should be interpreted as associative evidence within a single case context rather than causal validation of the framework.},
}

@article {pmid42992642,
year = {2026},
author = {Ingawale, S and Suvvari, TK and Giri, S and Moghe, A},
title = {What we owe patients: honest conversations about antibiotics and the microbiome.},
journal = {Future microbiology},
volume = {},
number = {},
pages = {1-4},
doi = {10.1080/17460913.2026.2756540},
pmid = {42992642},
issn = {1746-0921},
}

@article {pmid42992718,
year = {2026},
author = {Zhang, J and Ji, M and Lv, N and Zhou, Y},
title = {Cervicovaginal microbiome modulates HPV genotype-specific clearance/persistence: role of bacterial dysbiosis in cervical carcinogenesis.},
journal = {Annals of medicine},
volume = {58},
number = {1},
pages = {2754577},
doi = {10.1080/07853890.2026.2754577},
pmid = {42992718},
issn = {1365-2060},
mesh = {Female ; Humans ; *Dysbiosis/microbiology ; *Microbiota/genetics ; *Papillomavirus Infections/microbiology/virology/epidemiology ; *Uterine Cervical Neoplasms/microbiology/virology/epidemiology/pathology ; Genotype ; *Vagina/microbiology/virology ; *Cervix Uteri/microbiology/virology ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Uterine Cervical Dysplasia/microbiology/virology/epidemiology/pathology ; *Papillomaviridae/genetics/isolation & purification ; Carcinogenesis ; China/epidemiology ; Adult ; Longitudinal Studies ; },
abstract = {OBJECTIVES: This study focuses on the distinct epidemiological features of high-risk human papillomavirus (hrHPV) genotypes in Asian populations: HPV52/56/58 show uniquely high prevalence and strong correlation with cervical intraepithelial neoplasia, but their detection rates drop sharply in invasive cervical cancer, a pattern clearly different from the persistent dominance of HPV16/18 throughout malignant progression.

METHODS: To further elucidate the potential host-microbe interactions underlying these epidemiological observations, we integrated a 16S rRNA-sequenced cross-sectional discovery cohort and an independent longitudinal validation cohort from a Chinese population, with strict experimental quality control throughout the workflow.

RESULT: The preliminary analytical results demonstrate that a Lactobacillus-dominant cervicovaginal microbiome (CVM) is significantly and positively associated with HPV viral clearance, while enriched abundance of Gardnerella, Saccharofermentans and Atopobium exhibits a robust correlation with persistent HPV52/56/58 infection. Three undercharacterized microbial taxa-Chryseobacterium, Sphingobacterium and Enhydrobacter are closely linked to sustained HPV16/18 prevalence across advanced disease stages, and show negative correlation with the above obligate anaerobes, which aligns with the sharp decline of HPV52/56/58 in tumor tissues. A hormone-linked Chryseobacterium enrichment were also identified, a taxon with previously reported progesterone-degrading functional properties.

CONCLUSION: While further longitudinal studies are required to establish causal relationships, our results indicate that CVM dysbiosis may modulate the natural history of these high-burden HPV genotypes, and provide a foundational rationale for subsequent development of genotype-specific, microbiota-targeted cervical disease intervention strategies.},
}

Female
Humans
*Dysbiosis/microbiology
*Microbiota/genetics
*Papillomavirus Infections/microbiology/virology/epidemiology
*Uterine Cervical Neoplasms/microbiology/virology/epidemiology/pathology
Genotype
*Vagina/microbiology/virology
*Cervix Uteri/microbiology/virology
Cross-Sectional Studies
RNA, Ribosomal, 16S/genetics
*Uterine Cervical Dysplasia/microbiology/virology/epidemiology/pathology
*Papillomaviridae/genetics/isolation & purification
Carcinogenesis
China/epidemiology
Adult
Longitudinal Studies

@article {pmid42992834,
year = {2026},
author = {Gautam, A and Bhandari, D and Gurung, K and Gyawali, A and Gurung, K and Yadav, P and Smith, KCM and Ahmad, AR and Shrestha, D and Heugten, KA-v and Weyrich, LS and Karna, AK and Jha, AR},
title = {Industrialization restructures the domestic dog gut microbiome while preserving host specificity.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0086426},
doi = {10.1128/msystems.00864-26},
pmid = {42992834},
issn = {2379-5077},
abstract = {UNLABELLED: Industrialization has reshaped human gut microbiomes, but its effects on other human-associated mammals remain poorly understood. Domestic dogs provide an informative comparative system because they have shared human environments and food systems for millennia yet retain distinct host biology. However, most canine microbiome studies have focused on industrialized companion, colony, or controlled-feeding dogs, limiting our understanding of the ecological range of the domestic dog gut microbiome. We analyzed fecal 16S rRNA gene profiles from 261 dogs sampled across Nepal, Thailand, the United Arab Emirates, and the United States, spanning forager, agrarian, pastoralist, urban, and industrialized lifestyles; 257 dogs remained after excluding those with reported recent antibiotic exposure. Lifestyle was the strongest measured correlate of canine gut bacterial composition, and this association persisted in restricted analyses of mature, non-shelter dogs sampled from temperate regions. Industrialized dogs differed from non-industrialized dogs through directional genus-level shifts, prevalence-defined VANISH-like and BloSSUM-like bacterial guilds, coabundance structure, and shifts in predicted functional potential. Non-industrialized dogs were not microbiologically uniform: pastoralist dogs showed non-industrialized gut bacterial community profiles but diverged from a simple forager-to-industrialized continuum. Cross-species comparisons with humans sampled across matched lifestyle categories showed parallel lifestyle-associated restructuring in both hosts, but host species remained the dominant axis of variation, and genus-level responses were largely host specific. These findings expand the ecological baseline for canine gut bacterial communities and identify industrialization-associated lifestyle change as a major axis of gut bacterial community restructuring in a long-term human-associated mammal. More broadly, they show that shared lifestyle transitions can impose parallel ecological pressures across host species without overriding host-specific community assembly.

IMPORTANCE: Domestic dogs are one of the closest animal companions of humans, yet we know surprisingly little about how their gut microbiomes vary outside industrialized pet populations. This study shows that industrialization-associated lifestyle change is not only relevant to human microbiomes but also a broader ecological force that reshapes gut microbial communities in animals living alongside us. By comparing dogs across diverse human lifestyles, we show that shared environments can impose parallel pressures on the gut bacterial communities of humans and dogs, while each host maintains a distinct microbial identity. These findings suggest that gut microbial communities are shaped by the interaction between host biology and changing ecological conditions. Expanding microbiome research beyond industrialized settings is therefore essential for understanding what microbial diversity has been retained, altered, or lost during recent lifestyle transitions.},
}

@article {pmid42979986,
year = {2026},
author = {Rentzos, G and Fouka, E and Lazarinis, N and Gülen, T and Ramos-Ramirez, P and Flynn, L and Loukides, S and Xepapadaki, P and Papadopoulos, NG and Lindén, A and Bossios, A},
title = {Environmental Changes and Their Effect on the Airway Microbiome: Implications for Airway Diseases.},
journal = {Allergy},
volume = {},
number = {},
pages = {},
doi = {10.1111/all.70552},
pmid = {42979986},
issn = {1398-9995},
support = {20210286//Swedish Heart-Lung Foundation/ ; 20241637//Swedish Heart-Lung Foundation/ ; 20251269//Swedish Heart-Lung Foundation/ ; 20240343//Swedish Heart-Lung Foundation/ ; 2021-01527//Swedish Research Council/ ; 2024-0781//Region Stockholm/ ; },
abstract = {Obstructive airway diseases, including asthma and chronic obstructive pulmonary disease (COPD), represent the two major chronic airway inflammatory diseases. In both conditions, the airways are exposed to a variety of microbial and environmental stimuli. A healthy airway microbiome is characterized not only by microbial diversity but also by the absence of significant quantities of pathogens, and is signified by ecological stability, functional resilience, and balanced interactions with the host immune system. Although microbial diversity is often considered a marker of respiratory health, its association with disease depends on the anatomical site, host factors, and environmental exposures. Thus, microbial diversity alone should not be used as a universal marker of airway health-the occurrence of pathogens and the organ compartment are also factors that are important to consider. Disruption of this microbial homeostasis, known as dysbiosis, may involve reduced diversity of the commensal flora as well as increased quantity of key pathogens, and this condition is believed to stimulate inflammation that is associated with the progression of asthma and COPD, including exacerbations. Environmental changes, including air pollution, climate change, and urbanization, can disrupt microbial balance by reducing diversity and increasing the prevalence of pathogens. Several mechanisms contribute to this interaction, including damage to the airway epithelium, impaired mucociliary clearance, oxidative stress, and alterations in innate and adaptive immune responses. This review examines the interplay between external environmental factors and the airway microbiome, and how they affect airway obstructive diseases, asthma, and COPD to understand their immunopathology, and to improve disease prevention and treatment approaches. This is an area of great interest, and further research is required to elucidate these interactions so we can better help our patients.},
}

@article {pmid42980027,
year = {2026},
author = {Zhang, H and Zhu, L and Li, D and Yan, H and Yang, X and Zhou, Y},
title = {Microbiota-Derived Metabolites Mediate Immune Regulatory Networks in the Gut-Skin Axis of Psoriasis.},
journal = {Frontiers in bioscience (Landmark edition)},
volume = {31},
number = {10},
pages = {48099},
doi = {10.31083/FBL48099},
pmid = {42980027},
issn = {2768-6698},
support = {202101AZ070001-168//Yunnan Provincial Department of Science and Technology Applied Basic Research Joint Special Project/ ; XYLH2024053//Yunnan University of Chinese Medicine Joint University-Hospital Fund/ ; },
mesh = {Humans ; *Psoriasis/immunology/microbiology/metabolism ; *Gastrointestinal Microbiome/immunology ; *Skin/immunology/metabolism/microbiology ; Dysbiosis/immunology/microbiology ; Animals ; T-Lymphocytes, Regulatory/immunology ; Th17 Cells/immunology ; },
abstract = {Psoriasis is a chronic immune-mediated inflammatory disease affecting 2-3% people globally. Current biologic therapies targeting interleukin-23 and interleukin-17 pathways achieve only partial responses in most patients, highlighting the need for understanding upstream triggers. Emerging evidence implicates gut microbiome dysbiosis as a notable contributor to psoriasis pathogenesis through metabolite-mediated immune regulation. Psoriasis patients exhibit characteristic gut microbial alterations, including depletion of beneficial commensals such as Faecalibacterium prausnitzii and expansion of proinflammatory taxa. These compositional changes are associated with altered profiles of immunomodulatory metabolites, including short-chain fatty acids, tryptophan-derived indole compounds, and secondary bile acids, which promote regulatory T-cell differentiation, enhance immune tolerance through aryl hydrocarbon receptor activation, and modulate metabolic-immunological pathways. Such metabolic alterations may impair regulatory T cell function, promote T helper 17 (Th17) differentiation, compromise intestinal barrier integrity, and influence tissue-resident memory T cells that perpetuate disease chronicity. This process facilitates bacterial product translocation that amplifies inflammation, thereby amplifing relationship is bidirectional; psoriatic skin inflammation reciprocally affects gut homeostasis through circulating inflammatory mediators, systemic immune cell activation, and neuroendocrine stress pathways. Recent clinical evidence demonstrates that biologic therapies normalize gut microbiome composition and reduce trimethylamine N-oxide levels, supporting bidirectional gut-skin communication. These interactions create self-perpetuating cycles, suggesting that therapeutic strategies interrupting this feedback loop may offer novel treatment approaches. This review synthesizes current evidence on metabolite-mediated immune regulatory networks linking gut microbiome dysbiosis to psoriatic inflammation, evaluates clinical trials of microbiome-targeted interventions, and discusses methodological challenges, regulatory considerations, and future research directions for clinical translation. Understanding these mechanisms may inform the development of microbiome-targeted therapeutic approaches.},
}

Humans
*Psoriasis/immunology/microbiology/metabolism
*Gastrointestinal Microbiome/immunology
*Skin/immunology/metabolism/microbiology
Dysbiosis/immunology/microbiology
Animals
T-Lymphocytes, Regulatory/immunology
Th17 Cells/immunology

@article {pmid42980145,
year = {2026},
author = {Aghdam, SA and De Souza, R and Brown, AMV},
title = {Metatranscriptomic profiling of active endophytic microbiome functions across diverse Musa cultivars.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0225626},
doi = {10.1128/spectrum.02256-26},
pmid = {42980145},
issn = {2165-0497},
abstract = {Plant-endophyte symbioses play important roles in plant health and resilience, but the active functions of endophytic microbiomes remain less characterized than those of soil and rhizosphere microbiomes. We used metatranscriptomic profiling of culture-free enriched endophytic microbiomes from seven Musa cultivars grown under shared environmental conditions to characterize active microbial taxa and functional annotations across sampled tissues. Because each genotype and tissue combination had only one metatranscriptomic sample, this pilot study focuses on the microbial transcripts and functions detected in each sample rather than testing for cultivar or tissue differences. Culture-free enrichment produced metatranscriptomic profiles across samples, including 5,434 taxonomic annotations, and 32,694 gene annotations from expressed microbial transcripts. Functional annotations included pathways involved in secondary metabolism, energy production, environmental information processing, transport systems, oxidative phosphorylation, nitrogen metabolism, quorum sensing, biofilm formation, and xenobiotic biodegradation. Several taxa, including Bradyrhizobium sp., were detected across multiple samples and linked to diverse functional annotations. Approximately 30-35% of sequence reads were annotated as hypothetical proteins, showing that the functions of many detected transcripts are still unknown. Correlation analysis also showed sample-level associations among detected pathway profiles. Overall, this pilot metatranscriptomic data set provides a resource for banana endophyte research and identifies candidate microbial taxa and functional pathways for future studies of plant-microbiome interactions and microbe-microbe relationships.IMPORTANCEEndophytic microbiomes can influence plant health, but their active roles inside banana tissues remain poorly characterized. Here, we used metatranscriptomic profiling of culture-free enriched endophytic microbiomes from seven Musa cultivars to identify microbial taxa and functional pathways detected across sampled tissues. Metatranscriptomic data characterized pathways related to metabolism, transport, microbial signaling, biofilm formation, nutrient cycling, and secondary metabolism, suggesting potential variation in active microbiome profiles among sampled plants. This work provides a pilot resource for banana endophyte research and may help guide future studies on how plant-associated microbiomes interact with their hosts, how microbes function together inside plant tissues, and how these relationships could be used for microbiome-based crop improvement.},
}

@article {pmid42980318,
year = {2026},
author = {Sun, GT and Du, X and Zhang, XT and Wang, HL and Jiao, Y and Zhang, B},
title = {Host Fitness in Gastrointestinal Oncology: Beyond Tumor Biology.},
journal = {Journal of visualized experiments : JoVE},
volume = {},
number = {237},
pages = {},
doi = {10.3791/74153},
pmid = {42980318},
issn = {1940-087X},
mesh = {Humans ; *Gastrointestinal Neoplasms/therapy/physiopathology ; },
abstract = {Patients with gastrointestinal cancers face site-specific threats to nutritional intake, muscle function, organ reserve, and recovery. This critical narrative review examines host fitness as an organizing concept for these vulnerabilities rather than as a validated composite score. A targeted PubMed update identified publications from 2022 through September 14, 2026, using gastrointestinal cancer terms combined with prehabilitation, microbiome-immunotherapy, geriatric assessment, exercise, and digital assessment terms, while retaining relevant foundational studies. The review distinguishes guideline-supported care from prognostic associations and research-stage applications. Geriatric and nutritional assessments can guide established supportive care, whereas computed tomography-derived body composition and inflammatory indices primarily provide prognostic information. Microbiome signatures, epigenetic clocks, and integrated digital models require further validation before they can guide treatment decisions. Intervention effects vary by tumor site and treatment phase: selected prehabilitation trials demonstrate short-term benefits, although findings remain inconsistent, while long-term exercise after adjuvant chemotherapy for colon cancer represents a distinct evidence base. An operational assessment protocol and multidisciplinary workflow are presented to link documented impairments with existing care pathways and repeated assessment. No host-fitness threshold is proposed for treatment escalation, de-escalation, or sequencing. Prospective studies should establish incremental predictive value and patient benefit beyond existing assessments before this integrated framework is used to support precision treatment decisions.},
}

Humans
*Gastrointestinal Neoplasms/therapy/physiopathology

@article {pmid42980419,
year = {2026},
author = {Wang, T and Wang, J and Huangfu, B and He, X and Huang, K},
title = {Allobaculum stercoricanis and Its Postbiotics Alleviate Dextran Sulfate Sodium (DSS)-Induced Colitis through the Regulation of theTLR4/NF-κB Signaling Pathway.},
journal = {Journal of agricultural and food chemistry},
volume = {74},
number = {43},
pages = {33790-33804},
doi = {10.1021/acs.jafc.6c01607},
pmid = {42980419},
issn = {1520-5118},
support = {NA//China Agricultural University/ ; },
mesh = {Animals ; Dextran Sulfate/adverse effects ; *NF-kappa B/genetics/metabolism/immunology ; *Toll-Like Receptor 4/genetics/metabolism/immunology ; Signal Transduction/drug effects ; *Colitis/genetics/chemically induced/drug therapy/metabolism/microbiology/therapy/immunology ; Mice ; Humans ; *Receptors, Cytoplasmic and Nuclear/genetics/metabolism/immunology ; *Probiotics/administration & dosage ; Receptor, Farnesoid X-Activated ; Mice, Inbred C57BL ; Male ; Gastrointestinal Microbiome ; },
abstract = {Inflammatory bowel disease (IBD) is a chronic intestinal disorder that has become a global public health concern. Postbiotics offer advantages in biosafety and reproducibility over probiotics. Here, we demonstrated that live Allobaculum stercoricanis (A. stercoricanis) and its two postbiotic preparations─inactivated bacterial cells (POST) and cell-free fermentation supernatant (CFS)─effectively alleviated dextran sulfate sodium (DSS)-induced colitis in mice. Integrated gut microbiome and serum metabolomics analyses indicated that these interventions may act through modulating bile acid metabolism and Toll-like receptor signaling pathways. Further investigations combining postbiotic metabolomics, network pharmacology, molecular docking, and molecular dynamics simulations identified α-muricholic acid (α-MCA) as a candidate functional metabolite, with the farnesoid X receptor (FXR) as a potential target. We hypothesize that α-MCA may contribute to ameliorating intestinal inflammation through engagement of FXR and suppression of the TLR4/NF-κB signaling pathway. These findings provide new insights into postbiotic-based therapeutic strategies for IBD.},
}

Animals
Dextran Sulfate/adverse effects
*NF-kappa B/genetics/metabolism/immunology
*Toll-Like Receptor 4/genetics/metabolism/immunology
Signal Transduction/drug effects
*Colitis/genetics/chemically induced/drug therapy/metabolism/microbiology/therapy/immunology
Mice
Humans
*Receptors, Cytoplasmic and Nuclear/genetics/metabolism/immunology
*Probiotics/administration & dosage
Receptor, Farnesoid X-Activated
Mice, Inbred C57BL
Male
Gastrointestinal Microbiome

@article {pmid42980522,
year = {2026},
author = {Osman, MH and Wang, Q},
title = {The role of gut microbiota on the tumor microenvironment in colorectal cancer: a systematic review and meta-analysis.},
journal = {Minerva gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.23736/S2724-5985.26.03961-6},
pmid = {42980522},
issn = {2724-5365},
abstract = {BACKGROUND: This meta-analysis and systematic review examined gut microbial metabolites and the tumor microenvironment (TME) in colorectal cancer (CRC), as well as the influence of microbial metabolites on cancer development and treatment. The focus was on explaining how microbial metabolites influence cancer development and treatment outcome.

METHODS: A systematic search of PubMed, Embase, and the Cochrane Library was conducted (January 2010-December 2020) following the PRISMA 2020 guidelines.

RESULTS: Literature search yielded 765 articles, from which 22 studies were identified as meeting inclusion criteria after stringent screening. Included studies encompassed in vitro, in vivo, and patient-derived data on the role of gut microbial metabolites (e.g., short-chain fatty acids [SCFAs], bile acids, polyamines, and trimethylamine-N-oxide) in characterizing the CRC TME. Meta-analysis found that SCFAs, particularly butyrate, consistently played protective and regulatory functions, suppressing inflammation and stimulating antitumor immunity. In contrast, bile acids and certain microbial populations (e.g., Fusobacterium nucleatum) were associated with tumor-promoting pathways, including NF-κB and STAT3 activation. The overall result was moderately heterogeneous (I[2]=40%, P<0.05), reflecting variability in study design and metabolite focus. Publication bias testing with Egger's regression and funnel plots showed no indication of large small-study effects (P=0.21). Overall, 59% of studies reviewed cited a positive or modulatory function of metabolites in the TME, 27% proposed context-dependent or mixed effects, and 14% exhibited tumor-promoting activities. Moderate evidence strength, with limitations by virtue of preclinical and observational evidence, was present. Gut microbiota metabolites have context-dependent roles in CRC, SCFAs tending to be protective, and bile acids typically tumor-promoting.

CONCLUSIONS: The findings exhibit the therapeutic promise of microbiome-targeting treatments and dietary manipulation in modifying the TME. However, they remain to be confirmed by follow-up large-scale clinical trials to consolidate the evidence base.},
}

@article {pmid42980664,
year = {2026},
author = {Sohlberg, E and Laitila, A and Rämö, S and Sarlin, T},
title = {Fusarium Community Composition and Co-Occurrence with Other Fungi and Bacteria in Finnish Oat Crop.},
journal = {Microbial ecology},
volume = {89},
number = {1},
pages = {},
pmid = {42980664},
issn = {1432-184X},
mesh = {*Fusarium/isolation & purification/genetics/classification/metabolism ; *Avena/microbiology ; Finland ; *Bacteria/classification/isolation & purification/genetics ; *Microbiota ; Mycotoxins/analysis ; *Fungi/classification/isolation & purification/genetics ; Trichothecenes/analysis/metabolism ; Plant Diseases/microbiology ; },
abstract = {Fusarium species are major contributors to Fusarium head blight (FHB) and mycotoxin contamination in cereal production. To characterize microbial co-occurrence associated with toxin accumulation in oats, the Fusarium, fungal, and bacterial communities of 51 Finnish oat grain samples were analyzed using a multi-marker metabarcoding approach targeting Fusarium translation elongation factor 1‑alpha (EF1α), fungal ITS2, and bacterial 16S regions. Microbial profiles were compared between grains with high and low deoxynivalenol (DON) concentrations. High‑DON samples were dominated by F. graminearum, whereas F. langsethiae prevailed in low‑DON grains. Bacterial diversity was higher in high‑DON samples, while fungal diversity remained similar across groups. Several bacterial genera, including Pseudomonas, Paenibacillus, Massilia, and Curtobacterium, exhibited negative correlations with Fusarium species, indicating competition in the same niche, whereas Duganella and Xylophilus showed positive association with Fusarium abundance. Microdochium consistently co-occurred with Fusarium. Results show differences in microbial communities associated with mycotoxin levels and Fusarium community composition, identifying taxa that may influence FHB or indicate mycotoxin risk.},
}

*Fusarium/isolation & purification/genetics/classification/metabolism
*Avena/microbiology
Finland
*Bacteria/classification/isolation & purification/genetics
*Microbiota
Mycotoxins/analysis
*Fungi/classification/isolation & purification/genetics
Trichothecenes/analysis/metabolism
Plant Diseases/microbiology

@article {pmid42980681,
year = {2026},
author = {Gasner, N and Sweeney, M and Piché, JV and Doja, A and Bonakdar, R},
title = {Effects of Probiotics on Migraine in Children and Adults: A Systematic Review and Meta-Analysis.},
journal = {Current pain and headache reports},
volume = {30},
number = {1},
pages = {},
pmid = {42980681},
issn = {1534-3081},
mesh = {Humans ; *Probiotics/therapeutic use ; *Migraine Disorders/prevention & control ; Child ; *Gastrointestinal Microbiome/physiology ; Adult ; Female ; Treatment Outcome ; },
abstract = {PURPOSE OF REVIEW: Increasing evidence highlights a link between migraine, a disabling neurological disorder, and the gut microbiome. Probiotics, supplements containing colony-forming units of beneficial microbes, may influence migraine via the gut microbiome. A systematic review and meta-analysis of placebo-controlled trials was completed, and findings were synthesized narratively to evaluate probiotics for migraine prevention.

RECENT FINDINGS: Of 676 studies screened, 7 were included involving 612 participants (N = 487 females, 79.6%) consisting of 5 adult and 2 pediatric trials. Probiotics demonstrated a reduction in migraine severity on a 10-point scale (mean difference - 1.11; 95% CI - 2.26 to 0.03), monthly attack frequency (- 2.06; 95% CI - 3.6 to - 0.52), and disability (standardized mean difference - 0.86; 95% CI - 2.33 to 0.6). Certainty of evidence was graded very low. Probiotics may reduce migraine severity and frequency; however, the heterogeneity of studies limits generalizability. Despite the very low certainty of evidence, probiotics are safe and may reduce migraine as an adjunct preventative therapy.},
}

Humans
*Probiotics/therapeutic use
*Migraine Disorders/prevention & control
Child
*Gastrointestinal Microbiome/physiology
Adult
Female
Treatment Outcome

@article {pmid42980780,
year = {2026},
author = {Bhandari, SA and Kumari, P and Das, M},
title = {Regulatory T cells in atopic dermatitis: mechanisms of dysfunction, plasticity and therapeutic reprogramming.},
journal = {Inflammation research : official journal of the European Histamine Research Society ... [et al.]},
volume = {75},
number = {1},
pages = {},
pmid = {42980780},
issn = {1420-908X},
mesh = {Humans ; *T-Lymphocytes, Regulatory/immunology ; *Dermatitis, Atopic/immunology/therapy ; Animals ; Skin/immunology ; },
abstract = {OBJECTIVE AND DESIGN: This review focused on current evidence regarding the mechanisms underlying regulatory T cell (Treg) dysfunction in atopic dermatitis (AD), with particular emphasis on Treg instability, tissue microenvironmental reprogramming, inflammatory plasticity, and the skin-gut immune axis, and evaluated Treg-directed therapeutic strategies.

METHODS: Experimental and clinical studies investigating Treg functions, tissue microenvironment, immune regulation, microbial dysbiosis, and therapeutics in AD were critically analysed and integrated into a mechanistic framework.

RESULTS: AD is a chronic inflammatory skin disease with epidermal barrier dysfunction, pruritus, microbial dysbiosis, and immune dysregulation. Current evidence suggests that Treg abundance, phenotype, localization, and suppressive function may differ across AD endotypes and tissue compartments. Functional impairment or maladaptive plasticity might play a role in persistent inflammation within specific Treg populations. This may link to FOXP3 instability, altered IL-2/STAT5 signaling, metabolic strain, cytokine-induced destabilization, plasticity, keratinocyte-derived alarmins, inflammatory dendritic cells, Staphylococcus aureus colonization, and the skin-gut microbial axis. Novel therapeutics may restore immune tolerance beyond conventional anti-inflammatory treatment, including Treg-selective IL-2 agonists, microbiome-based therapy, and antigen-specific regulatory approaches.

CONCLUSION: Treg dysregulation may represent a major component in AD pathogenesis, but its causality for disease persistence and therapeutic reversibility is yet to be elucidated.},
}

Humans
*T-Lymphocytes, Regulatory/immunology
*Dermatitis, Atopic/immunology/therapy
Animals
Skin/immunology

@article {pmid42980890,
year = {2026},
author = {Yao, Y and Chen, X and An, X and Jiao, Y and Jiang, Q},
title = {From Macroenvironmental Context to Individual Proximal Exposure: Multiscale Mechanisms Linking Environmental Factors to Blood Pressure Homeostasis and Variability : Author.},
journal = {Cardiovascular toxicology},
volume = {26},
number = {11},
pages = {},
pmid = {42980890},
issn = {1559-0259},
mesh = {Humans ; Animals ; *Blood Pressure/drug effects ; *Hypertension/physiopathology/epidemiology/etiology/diagnosis/psychology ; *Environmental Exposure/adverse effects ; Homeostasis ; Risk Factors ; Risk Assessment ; *Social Determinants of Health ; },
abstract = {Hypertension is a major contributor to the global burden of cardiovascular disease. In addition to genetics, age, and lifestyle, environmental exposures can disrupt blood pressure homeostasis. Compared with air pollution and ambient temperature, evidence concerning psychosocial factors, noise, light, chemical pollutants, micro- and nanoplastics, and the individual proximal residential environment is more fragmented, and studies often conflate mean blood pressure, incident hypertension, and blood pressure variability (BPV) as equivalent outcomes. Using a continuum from macroenvironmental context to individual proximal exposure, this review integrates evidence from human studies, animal experiments, and in vitro research to compare associations of air pollution, temperature, greenspace, noise, chemical pollutants, micro- and nanoplastics, light exposure, and psychosocial stress with distinct blood pressure phenotypes. We further summarize shared pathways involving autonomic and neurohumoral regulation, oxidative stress-inflammation-endothelial injury, the renin-angiotensin-aldosterone system (RAAS), circadian rhythms, and metabolic/microbiome mechanisms. Human evidence is relatively substantial for air pollution, temperature, noise, and greenspace, whereas direct evidence linking micro- and nanoplastics and some chemical pollutants to human hypertension and BPV remains limited, with mechanistic understanding derived mainly from experimental models. Multiple exposures, genetic and epigenetic backgrounds, and socioeconomic conditions may jointly modify environmental effects. Clarifying exposure dose, level of evidence, and the relevant BPV time scale will help identify environmentally susceptible populations and provide a conceptual basis for stratified prevention and future intervention studies.},
}

Humans
Animals
*Blood Pressure/drug effects
*Hypertension/physiopathology/epidemiology/etiology/diagnosis/psychology
*Environmental Exposure/adverse effects
Homeostasis
Risk Factors
Risk Assessment
*Social Determinants of Health

@article {pmid42981088,
year = {2026},
author = {Chen, G and Du, S and Li, H and Wang, H and Zhu, H and Zhang, Q and Yang, R and Wu, X and Shao, B and Zhang, Y},
title = {Multi-matrix metabolome and microbiome profiling in diarrhea-predominant irritable bowel syndrome and ulcerative colitis in remission with IBS-like symptoms.},
journal = {Inflammatory bowel diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/ibd/izag243},
pmid = {42981088},
issn = {1536-4844},
support = {2025YFC3408601//the National Key Research and Development Program/ ; 2022-HX-6//China Health and Medical Development Foundation/ ; },
abstract = {BACKGROUND: Irritable bowel syndrome (IBS)-like symptoms frequently persist in patients with ulcerative colitis (UC) in remission. Whether UC in remission with IBS-like symptoms (UCR-IBS) represents functional overlap with diarrhea-predominant IBS (IBS-D) or a distinct metabolic phenotype remains unclear.

METHODS: In this exploratory cross-sectional study, 39 patients with IBS-D, 21 with UCR-IBS, and 35 healthy controls were enrolled. Serum, urine, fecal, and colonic mucosal samples were collected. Untargeted metabolomics, targeted tryptophan profiling, fecal 16S ribosomal RNA gene sequencing, predicted microbial functional profiling, and microbe-metabolite association analyses were performed.

RESULTS: Tryptophan-related metabolism was altered in both patient groups, but the patterns differed across biological matrices. Compared with IBS-D, UCR-IBS showed higher serum N-formylkynurenine (NFK) concentrations, and fecal findings suggested reduced concentrations of microbiota-associated indole metabolites. Microbiome differences were modest, but predicted nicotinate/nicotinamide metabolism was enriched in UCR-IBS. Exploratory network analysis identified associations between tryptophan-related metabolites and selected bacterial genera in each group.

CONCLUSIONS: Multi-matrix profiling shows tryptophan-related metabolic differences between mesalazine-treated UCR-IBS and IBS-D, highlighting higher serum NFK concentrations in UCR-IBS. These findings provide a basis for investigating host-microbiota metabolic relationships across systemic and intestinal compartments during UC remission.This trial was registered in the Chinese Clinical Trial Registry (ChiCTR; https://www.chictr.org.cn/) under registration number ChiCTR2200060224.},
}

@article {pmid42981279,
year = {2026},
author = {Chen, J and Cheng, YQ and Fan, LP and Zhou, X and Jiang, JY and Wu, F and Liang, PW and Liu, Y and Zuo, ZL and Zhu, GX},
title = {Environmental enrichment is associated with changes in the gut microbiome and resistome of captive pythons.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0360735},
pmid = {42981279},
issn = {1932-6203},
mesh = {Animals ; *Boidae/microbiology ; *Gastrointestinal Microbiome/genetics ; Environment ; Metagenomics ; },
abstract = {Environmental enrichment is widely used to improve the welfare of captive animals, yet its effects on reptilian gut microbiota remain poorly understood. Here, we used shotgun metagenomic sequencing to investigate the gut microbiome and resistome of two captive python species: Burmese python (Python bivittatus) and reticulated python (Malayopython reticulatus), before and after environmental enrichment. We found that environmental enrichment was associated with increased α-diversity in Burmese pythons, as indicated by significantly higher ACE and observed species indices, while NMDS ordination revealed differences in the observed patterns of community composition between the two species. Pseudomonadota and Bacteroidota were dominant phyla in the gut microbiota of both python species, but their relative abundances responded differently to enrichment between hosts. Functional analyses suggested an enhanced metabolic potential in Burmese pythons, particularly in carbohydrate metabolism and environmental information processing, accompanied by increased abundance of carbohydrate-active enzymes. In addition, enrichment may influence the gut resistome, with Pseudomonadota contributing the majority of antibiotic resistance genes. Overall, our results demonstrate that environmental enrichment measures, such as dietary changes and improvements in water and air quality, are associated with changes in the gut microbiome and resistome of captive pythons in a host-dependent manner, highlighting the combined roles of diet and environmental conditions in the observed changes in the gut microbiota. These findings provide exploratory insights into the functional responses and host-microbiome evolution of reptile gut microbiota to captivity and have important implications for the management and welfare of captive animals.},
}

Animals
*Boidae/microbiology
*Gastrointestinal Microbiome/genetics
Environment
Metagenomics

@article {pmid42981365,
year = {2026},
author = {Mogire, DB and Neondo, J and Muhonja, C and Awuor, C and Mureithi, D and Ogada, S and Wekesa, TB},
title = {Metagenomic analysis of tomato rhizosphere microbiomes detects Ralstonia phage sequences in Kenyan agricultural soils.},
journal = {PloS one},
volume = {21},
number = {11},
pages = {e0362106},
pmid = {42981365},
issn = {1932-6203},
mesh = {*Solanum lycopersicum/microbiology ; *Rhizosphere ; Kenya ; *Bacteriophages/genetics ; *Soil Microbiology ; *Microbiota/genetics ; *Metagenomics/methods ; *Ralstonia/virology/genetics ; Phylogeny ; Metagenome ; *Ralstonia solanacearum/virology ; Agriculture ; },
abstract = {Bacterial wilt caused by Ralstonia solanacearum species complex is a major constraint in tomato production in Kenya, resulting in yield losses of up to 100% in heavily infested fields. This study used high-throughput shotgun metagenomic sequencing approach to characterize the rhizosphere microbiomes of tomato plants in three of the major production areas in Kenya (Kirinyaga, Kiambu, and Laikipia counties) focusing on detecting Ralstonia phage sequences. Soil samples were collected from the rhizosphere of bacterial wilt-infected tomato plants, and microbial DNA was extracted using a modified phenol-chloroform protocol and sequenced using Illumina NovaSeq platform. Taxonomic profiling revealed diverse microbial communities dominated by Actinobacteria and Proteobacteria. Four Ralstonia species were confirmed (R. insidiosa, R. pickettii, R. mannitolilytica and R. wenshanensis). Sequences similar to the R. solanacearum species complex were also detected but were too short for species-level confirmation. Metagenomic analysis detected sequences matching four previously described Ralstonia phages (RSL1, RSIBR3, Anchaing, and Cimandef). Functional annotation demonstrated abundant metabolic pathways, energy production systems, and stress response mechanisms, indicating highly adaptive microbial communities in the tomato rhizosphere. This study provides baseline data on rhizosphere microbiome composition in Kenyan tomato production systems and identifies Ralstonia phage sequences that could guide future isolation and host-range studies. If future work shows that these phages are active against Ralstonia, they could contribute to locally adapted biocontrol approaches that reduce reliance on chemical pesticides.},
}

*Solanum lycopersicum/microbiology
*Rhizosphere
Kenya
*Bacteriophages/genetics
*Soil Microbiology
*Microbiota/genetics
*Metagenomics/methods
*Ralstonia/virology/genetics
Phylogeny
Metagenome
*Ralstonia solanacearum/virology
Agriculture

@article {pmid42981424,
year = {2026},
author = {de Souza, MR and Bruce, J and Cros, A and Jury, CP and Drury, C and Toonen, RJ},
title = {Stony coral symbioses show variable responses to future ocean conditions.},
journal = {Science advances},
volume = {12},
number = {45},
pages = {eaed4599},
pmid = {42981424},
issn = {2375-2548},
mesh = {Animals ; *Symbiosis ; *Anthozoa/physiology/microbiology ; Coral Reefs ; *Oceans and Seas ; Ecosystem ; Biodiversity ; Microbiota ; },
abstract = {Coral reefs support over a quarter of marine species and nearly a billion people worldwide but are also among the ecosystems most threatened by anthropogenic impacts. There is long-standing debate about whether coral symbioses will be disrupted or respond adaptively under future ocean conditions. Using a factorial 2.5-year future-ocean mesocosm experiment across eight coral species representing the major coral lineages, we tracked symbiont community shifts within replicate fragments from the same individual coral. Some corals exhibited stochastic divergence, whereas others showed deterministic shifts in symbiont community composition. Heat stress generally reduced symbiont diversity and promoted predictable restructuring, consistent with deterministic adaptation to moderate thermal stress but stochastic accumulation of diversity under extreme conditions. We propose that adaptive and stochastic responses represent endpoints along a continuum of host-orchestrated symbiont sorting. This study bridges coral reef ecology with broader host-microbiome theory, offering an integrated perspective on how symbiotic systems may respond to environmental change.},
}

Animals
*Symbiosis
*Anthozoa/physiology/microbiology
Coral Reefs
*Oceans and Seas
Ecosystem
Biodiversity
Microbiota

@article {pmid42981479,
year = {2026},
author = {Kim, SG and Venzon, M and Jacobs, JP},
title = {Probiotics for Human Health: Mechanisms, Clinical Evidence, Risks, and Next-Generation Microbial Therapeutics.},
journal = {Annual review of physiology},
volume = {},
number = {},
pages = {},
doi = {10.1146/annurev-physiol-040425-041450},
pmid = {42981479},
issn = {1545-1585},
abstract = {Probiotics are widely used live microbial supplements intended to promote human health, yet their clinical benefits remain inconsistent and often strain-specific. Most currently available probiotics are derived from Lactobacillus, Bifidobacterium, and Saccharomyces species originally isolated from fermented foods or human microbiota. Preclinical studies suggest that these organisms may influence host physiology through several mechanisms, including antimicrobial activity, toxin inhibition, strengthening of intestinal barrier function, modulation of immune responses, and signaling along the gut-brain axis. However, translation of these mechanisms into consistent clinical benefit has been limited by heterogeneity in probiotic strains, dosing, and study design. Emerging evidence also highlights potential unintended consequences of probiotic use, including rare infections in vulnerable patients, alterations of microbiome recovery after antibiotics, and possible interactions with host metabolism or medications. Recent advances in microbiome research have supported the development of next-generation probiotics and engineered microbial therapeutics, representing a shift toward more targeted and mechanistically informed live microbial therapies.},
}

@article {pmid42981630,
year = {2026},
author = {Erdoğan, Y and Özgen, EK and Polat, B and Çolak, A and Çomaklı, S and Bolat, İ and Celep, L and Çiplak, AY and Elban, Ş and Aydın, Ş and Yolcu, K and Çinpolat, A and Öztürkler, O},
title = {Uterine microbiota across cytological severity of subclinical endometritis in Simmental cows: a full-length 16S rRNA nanopore study.},
journal = {Theriogenology},
volume = {269},
number = {},
pages = {118301},
doi = {10.1016/j.theriogenology.2026.118301},
pmid = {42981630},
issn = {1879-3231},
abstract = {Subclinical endometritis (SE) reduces fertility in dairy cows without clinical signs. In this cross-sectional study we compared the uterine microbiota of cows with SE and cytologically healthy cows, and examined how it varies across cytological severity, using full-length 16S rRNA nanopore sequencing. Uterine cytobrush samples were collected 48 to 62 days postpartum from Simmental cows in 24 herds and graded cytologically (score 0 to 3) using thresholds defined a priori. Of 137 cows with a valid score, 105 were included in the primary analysis after 24 cows with fewer than 1000 bacterial reads and eight cows with discordant diversity were excluded. Alpha diversity was higher in cows with SE than in cytologically healthy cows (mean Shannon 3.26 vs 3.03; p: 0.026) and was significantly correlated with the score (ρ: 0.22; p: 0.027), but did not differ among the three SE scores. Community structure differed between the groups (Bray-Curtis PERMANOVA R[2]: 0.036; p: 0.014), and pairwise comparisons showed significant differences between score 0 and scores 1 and 3, but not among the SE scores. Genera with a higher relative abundance in SE included gut-associated anaerobes such as Paeniclostridium and Mogibacterium, whereas genera with a higher relative abundance in healthy cows were environmental taxa that also dominated the negative control. The differences between healthy and SE cows were not significant when herd or sequencing library was accounted for. Herd explained 46% of the variation in community structure (p: 0.001). Classical uterine pathogens were rare, and Trueperella spp. were detected only at trace levels. Full-length 16S sequencing across four grades of cytological severity showed that diversity and community structure differed between cytologically healthy and SE cows but not among the SE scores, that this difference was not significant after adjustment for herd or sequencing library, and that herd had a significant effect on the uterine microbiota.},
}

@article {pmid42981705,
year = {2026},
author = {McMillan, R and Dria, RM and Moreau, GB and Ma, JZ and Siraj, MS and Shakil, MM and Billah, SM and Petri, WA and Haque, R and Madden, GR},
title = {First-Trimester Maternal Gut Microbiome and Small Vulnerable Newborns: A Prospective Cohort Study.},
journal = {BJOG : an international journal of obstetrics and gynaecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1471-0528.70356},
pmid = {42981705},
issn = {1471-0528},
support = {AI043596//National Institute of Allergy and Infectious Diseases/ ; T32AI055432//National Institute of Allergy and Infectious Diseases/ ; UG1 HD096730//Eunice Kennedy Shriver National Institute of Child Health and Human Development/ ; },
abstract = {OBJECTIVES: To investigate the relationship between the first trimester gut microbiome and small vulnerable newborns (SVN).

SETTING: Rural low- and middle-income country: Bangladesh.

POPULATION: 213 women were enrolled during the first trimester of pregnancy as part of the NICHD Global Network for Women's and Children's Health registry, Bangladesh.

METHODS: Observational study of the maternal gut microbiome and birth outcomes. Blood and stool samples were collected at enrollment. Birth outcomes were recorded within 72 h of delivery. Random forest machine learning models trained on microbiome data were used to predict SVN or first-trimester maternal features of interest. Hold out sets were used to test model accuracy.

MAIN OUTCOME MEASURES: SVN (born preterm, low birth weight, or small for gestational age).

RESULTS: The birth outcome SVN (n = 106) was discriminated from non-SVN (n = 107) using a microbiome-trained random forest model (AUC = 0.653, 95% CI 0.518-0.789). The microbiome also predicted the inflammatory markers plasma alpha-1-acid glycoprotein and faecal calprotectin (AUC = 0.742, 95% CI: 0.616-0.868 and AUC = 0.793, 95% CI: 0.680-0.905, respectively), while micronutrient concentrations, anaemia, C-reactive protein and the presence of atypical Enteropathogenic E. coli were not reliably predicted. Higher alpha-1-acid glycoprotein was significantly associated with SVN (aOR = 1.98; 95% CI: 1.04-3.85) whereas calprotectin was not.

CONCLUSIONS: In this prospective cohort, first-trimester maternal gut microbiome composition showed modest discrimination for SVN and a marker of systemic inflammation. These findings support further investigation of early pregnancy microbiome-inflammation pathways in fetal growth restriction and preterm birth.},
}

@article {pmid42981716,
year = {2026},
author = {Bhimavarapu, K and Williams, GR and Cooley, M and Santana-Pereira, ALR and Price, AJ and Price, SB and Huber, L},
title = {Current and emerging threats to honey bee health: a One Health perspective on antibiotic pollution.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-9},
doi = {10.2460/javma.26.07.0607},
pmid = {42981716},
issn = {1943-569X},
abstract = {Pollinators play a critical role in global food production and ecosystem health, yet high losses of essential honey bee colonies have been reported worldwide. Climate change, habitat loss, parasites, pesticides, and poor nutrition are established pollinator threats, whereas environmental antibiotic pollution remains poorly understood. Antibiotic exposure may independently affect bees or interact with these stressors, potentially compounding adverse health effects. Synthetic antibiotic residues and resistance genes enter the environment through the fertilization of soils with antibiotic-containing animal manure, animal wastewater discharge, and airborne antibiotic contamination landing directly on flowers and crops. While the effects of direct antibiotic exposure on honey bees have been studied, the consequences of indirect environmental exposure remain largely unknown. Foraging bees may encounter antibiotic contaminants in the environment, potentially disrupting their gut microbiome, altering behavior and physiology, and increasing susceptibility to pathogens. Contamination of honey bees and their products with antibiotics serve not only as indicators of environmental antibiotic resistance but also as a practical One Health model linking human, animal, and environmental health. Studying honey bee responses to agricultural contaminants provides insight into how antibiotic resistance and environmental stressors can move across ecosystems, affecting both pollinators and the broader public. This review synthesizes current knowledge on the multifactor threats to honey bees and their mitigation strategies, emphasizing the influence of animal production and antibiotic pollution on honey bee health. We highlight knowledge gaps in understanding the transfer of antibiotic resistance from agricultural environments to honey bees to enhance pollinator health and promote long-term ecological resilience.},
}

@article {pmid42981773,
year = {2026},
author = {Korkmaz, HI and Boer, DP and van der Ven, F and Meeder, M and Papendorp, S and Pijpe, A and Vries, AM and Bosma, E and van Zuijlen, PPM},
title = {Immune function in burn patients: Pathophysiology, monitoring, and emerging therapeutic strategies.},
journal = {Burns : journal of the International Society for Burn Injuries},
volume = {52},
number = {9},
pages = {108260},
doi = {10.1016/j.burns.2026.108260},
pmid = {42981773},
issn = {1879-1409},
abstract = {Severe burn injury causes extensive local tissue damage and systemic immune alterations that affect infection risk, wound healing, organ function, and survival. The immune response is characterized by rapid activation of innate immune cells, including neutrophils and monocytes, with elevated pro-inflammatory cytokines (IL‑6, TNF‑α, IL‑1β) and complement activity. Simultaneously, adaptive immunity is often impaired, with reduced T and B lymphocyte function, while diminished dendritic cell activity may further compromise antigen presentation and adaptive immune responses. This combined hyperinflammatory and immunosuppressive state, known as burn-induced immune dysfunction, contributes to delayed wound healing, increased susceptibility to secondary infections, sepsis, and multiple organ dysfunction. Monitoring immune function is essential but challenging. Routine markers, including white blood cell count (WBC) and C-reactive protein (CRP), provide limited insight, whereas procalcitonin (PCT), pancreatic stone protein (PSP), and cytokine panels (IL‑6, IL‑8, IL‑10) improve early detection of infection and immune classification. Flow cytometry allows characterization of immune cell populations and functional markers such as monocyte HLA‑DR and T cell PD‑1, while functional assays assess neutrophil, monocyte, and lymphocyte responsiveness. High-resolution molecular approaches, including transcriptomics, proteomics, and single-cell profiling, reveal persistent alterations not captured by conventional assays. Therapeutic strategies to restore immune balance include targeted cytokine modulation, immune checkpoint inhibition, hemoadsorption, metabolic and nutritional interventions, and novel approaches such as nanotechnology or microbiome modulation. Early surgical excision and topical treatments, including cerium-nitrate with silver sulfadiazine, may also attenuate systemic inflammation. However, robust clinical evaluation of these interventions is limited, and their timing, dosing, and patient selection remain under investigation. This review integrates mechanistic, translational, and clinical evidence to provide a framework for understanding burn-induced immune dysfunction. Future research should aim for standardized immune phenotyping, longitudinal multi-omics integration, AI-assisted monitoring, and evaluation of mechanism-based immunomodulatory strategies to improve patient outcomes.},
}

@article {pmid42981844,
year = {2026},
author = {Jeong, M and Yeo, S and Kang, D and Park, S and Hyun, Y and Jeong, SY and Shin, JH and Lee, S},
title = {Antibiotic resistance gene classes show no detectable shift despite extensive microcystin-associated river microbiome reorganization.},
journal = {Water research},
volume = {309},
number = {Pt B},
pages = {127235},
doi = {10.1016/j.watres.2026.127235},
pmid = {42981844},
issn = {1879-2448},
abstract = {Antibiotic resistance gene (ARG) signals can reflect increasing environmental resistance or changes in the microorganisms carrying those genes. Cyanobacterial blooms make this distinction especially important because they can reorganize entire freshwater microbial communities. We combined repeated metagenomic sampling at ten sites over eleven rounds along an 85 km Nakdong River reach with taxonomic, functional, and genome-resolved analyses and site-aware machine learning. Sampling round explained 60.9% of microbial-community variation, compared with 5.0% for site, indicating that temporal turnover dominated persistent spatial structuring. After adjusting for site, season, and water temperature, high-microcystin conditions were associated with 3,241 microbial features. None of the 18 tested ARG drug classes showed a corresponding association. The resistance-candidate inventory sums candidate annotations in representative metagenome-assembled genomes (MAGs) assigned to origin samples; drug-class profiles partition the same annotations rather than measuring sample-wide ARG abundance. Across 301 representative MAGs, candidate counts were strongly positively associated with genome size, indicating that the inventory partly reflected the microbial genomic content represented. In exploratory models, predicted resistance-candidate inventories differed between community states. High-microcystin conditions therefore coincided with extensive microbial reorganization without a detectable parallel ARG-class response. Microcystin measurements should be paired with direct ARG measurements and community profiles to track toxin hazard, resistance determinants, and microbial turnover.},
}

@article {pmid42981905,
year = {2026},
author = {Hu, J and He, Y and Cui, W and Wei, L and Li, L and Wang, L and Alwathnani, H and Rensing, C and Zhang, J},
title = {Halophyte-derived rhizosphere microbiome transplantation improves physiological homeostasis and salt tolerance in alfalfa.},
journal = {Microbiological research},
volume = {315},
number = {},
pages = {128801},
doi = {10.1016/j.micres.2026.128801},
pmid = {42981905},
issn = {1618-0623},
abstract = {Halophyte-associated microbiomes are promising reservoirs of stress-adapted microorganisms, yet the consequences of transferring whole rhizosphere communities to phylogenetically distinct crops have remained unclear. Here, we evaluated rhizosphere microbiome transplantation (RMT) from Suaeda salsa to alfalfa (Medicago sativa) in a 2 × 2 factorial experiment comprising control and RMT treatments at 0 and 300 mM NaCl. Plant physiological responses were integrated with metagenomic profiling, community assembly analysis, microbial association networks, and functional gene analyses. Under salinity, RMT increased plant height, leaf area, and both shoot and root biomass, reduced shoot Na[+] accumulation, and increased the shoot K[+]/Na[+] ratio. RMT also reduced H2O2, malondialdehyde, and relative electrical conductivity while increasing antioxidant enzyme activities and osmolyte concentrations, whereas gas-exchange parameters showed no significant recovery. RMT altered rhizosphere community composition and assembly and was associated with greater network connectivity and simulated robustness. Metagenomic KO profiles showed higher relative representation of functions correlated to osmoprotection, ion transport, redox protection, and cell-envelope processes. These microbial functional shifts coincided with the physiological domains most strongly improved by RMT but did not establish direct causal microbial mechanisms. Overall, halophyte-derived RMT improved alfalfa performance under salinity, with coordinated physiological recovery accompanied by substantial reorganization of the recipient rhizosphere, supporting further evaluation of whole-community microbiome transplantation for crop production in saline soils.},
}