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        <title>Frontiers in Microbiomes | New and Recent Articles</title>
        <link>https://www.frontiersin.org/journals/microbiomes</link>
        <description>RSS Feed for Frontiers in Microbiomes | New and Recent Articles</description>
        <language>en-us</language>
        <generator>Frontiers Feed Generator,version:1</generator>
        <pubDate>2026-07-08T13:13:59.351+00:00</pubDate>
        <ttl>60</ttl>
        <item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1860559</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1860559</link>
        <title><![CDATA[Artificial intelligence in soil microbiome-driven agriculture: from practical limits to a translational roadmap]]></title>
        <pubdate>2026-07-03T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Acharya Balkrishna</author><author>Priyanka Chaudhary</author><author>Shelly Singh</author><author>Anishka Saini</author><author>Aditi Kumari</author><author>Khushi Ishika Mahato</author><author>Vedpriya Arya</author>
        <description><![CDATA[BackgroundSoil microbiome research has been revolutionized by advances in high-throughput sequencing and multi-omics technologies, generating massive datasets that capture the taxonomic, functional, and metabolic diversity of microbial communities in agricultural soils; however, interpreting these complex datasets and translating them into practical agronomic insights remains challenging.ObjectivesTo critically assess the role of artificial intelligence (AI) in soil microbiome-driven agriculture, focusing on methodological developments, prediction performance, existing limitations, and translational opportunities.MethodsA narrative review was conducted to evaluate commonly used AI approaches, including random forest, gradient boosting, support vector machines, and deep learning architectures, alongside key microbiome data types such as amplicon sequencing, metagenomics, and functional gene profiling, with integration of environmental, agronomic, and meteorological datasets.ResultsThe prediction of crop productivity, disease risk, nutrient cycling dynamics, and soil health indicators may be enhanced by AI-assisted integration of microbiome, soil physicochemical, and meteorological data, according to several studies. However, broad generalizations about predictive robustness and generalizability are limited by significant diversity in datasets, validation methods, and model architectures.DiscussionTo address these limitations, a five-phase implementation framework integrating centralized data systems, AI-driven analytics, multi-omics profiling, standardized soil sampling, and feedback-based model retraining within precision agriculture systems is proposed, providing a pathway for translating microbiome insights into field-scale decision support.ConclusionAI-enabled soil microbiome applications hold significant potential for sustainable agriculture, but future advancements will require large, multisite datasets, improved validation strategies, interpretable modeling approaches, and integration with digital agriculture technologies, highlighting both opportunities and practical constraints.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1832151</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1832151</link>
        <title><![CDATA[Nasal cavity microbial makeup and the influence on psychiatric symptoms following fire exposure in firefighters]]></title>
        <pubdate>2026-06-23T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Paul Grunsted</author><author>Chao Xu</author><author>Amanda Janitz</author><author>Jessica Reese</author><author>Janis Campbell</author><author>Tasha M. Santiago-Rodriguez</author><author>Sara J. Javornik Cregeen</author><author>Joseph F. Petrosino</author><author>Jooyeon Hwang</author>
        <description><![CDATA[BackgroundFirefighters experience high levels of occupational stress and trauma, increasing their risk of depression, anxiety, and post-traumatic stress disorder (PTSD). Although microbial communities may influence brain function and behavior through neural pathways, the nasal microbiome remains understudied. This study examined associations between nasal microbiome characteristics and psychiatric symptoms among firefighters.MethodsWe conducted a cross-sectional study of 34 firefighters recruited from Texas fire stations. Participants completed validated questionnaires assessing depression, anxiety, and PTSD. Nasal swabs were collected before and after fire suppression and 16S rRNA sequencing was used to characterize microbial communities. Alpha and beta diversity, relative abundance, and differential microbial associations with psychiatric outcomes were assessed using logistic, linear, and linear mixed regression methods.ResultsSixteen participants (47%) met criteria for depression, six (18%) for anxiety, and four (12%) for PTSD. Alpha diversity was significantly lower in individuals with anxiety (adjusted p = 0.04) while there were no differences in beta diversity or differences in either diversity for PTSD or depression. Increased abundance of the genus Ruminococcus was associated with increased odds of anxiety, while Hydrotalea was associated with PTSD. Depression scores were positively associated with several genera including Aerococcus (1.22; 95%CI: 0.43-2.02) and Dermabacter (1.50; 95% CI: 0.37-2.63). Fire suppression was associated with increased Enhydrobacter (2.08; 95% CI: 0.80 to 3.46) and decreased Hymenobacter (-1.25; 95% CI: -2.22 to -0.27) abundance.ConclusionsThis study identifies preliminary links between nasal microbiome composition and psychiatric symptoms in firefighters and suggests that fire suppression may alter nasal microbial communities.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1863308</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1863308</link>
        <title><![CDATA[Fecal microbiota transplantation: from empirical remedy to precision medicine]]></title>
        <pubdate>2026-06-17T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Junsheng Zhao</author><author>Yiming Fan</author><author>Keda Yang</author><author>Hainv Gao</author>
        <description><![CDATA[Fecal microbiota transplantation (FMT) has evolved from an empirical remedy for recurrent Clostridioides difficile infection (rCDI) into a foundational platform for precision microbiome-based therapeutics. This comprehensive review details FMT’s journey, analyzing its multifaceted mechanisms of action—including restoration of colonization resistance, metabolic reprogramming via short-chain fatty acids and bile acids, and profound immunomodulation—which extend far beyond simple microbial replacement. We critically evaluate its established, high efficacy in rCDI and its expanding, albeit more variable, applications across a wide spectrum of gastrointestinal diseases (such as inflammatory bowel disease, irritable bowel syndrome, and constipation), neurological disorders (including Parkinson’s and Alzheimer’s disease), metabolic conditions, autoimmune diseases, and oncology (particularly in modulating response to immune checkpoint inhibitors and treating graft-versus-host disease). The review further discusses the critical challenges of donor-recipient variability, safety, and the lack of standardized protocols that have driven the field’s technical evolution. This progression encompasses refined processing methods like washed microbiota transplantation (WMT), diverse delivery routes including oral capsules, and the exploration of non-bacterial components like bacteriophages through fecal filtrate transplantation (FVT). Ultimately, we highlight the field’s trajectory toward next-generation, defined live biotherapeutic products (LBPs) and engineered microbial consortia, aiming to transition from the complex “black box” of whole stool to safer, more consistent, and rationally designed precision therapies that target the specific dysbiotic networks underlying diverse human diseases.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1820309</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1820309</link>
        <title><![CDATA[Variation in cloacal microbiota of Canada goose (Branta canadensis) across rural and urban areas in Illinois, USA]]></title>
        <pubdate>2026-06-17T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Daniel B. Raudabaugh</author><author>Sara Villazan Perez-Girones</author><author>Nelda A. Rivera</author><author>Tooba Latif</author><author>Evan W. London</author><author>Nicole F. Pietrunti</author><author>Willian M. Brown</author><author>Nohra E. Mateus-Pinilla</author><author>Auriel M. V Fournier</author>
        <description><![CDATA[IntroductionThe cloacal microbiota of birds is shaped by host factors, diet, environmental exposure, and increasing overlap between wild bird habitats and human development may influence these communities. However, the effects of urbanization on herbivorous waterfowl in Illinois remain poorly understood.MethodsIn this study, we characterized the cloacal microbiota of 106 Canada goose (Branta canadensis) sampled from rural and urban areas in Illinois using 16S rRNA gene V4 amplicon sequencing, and evaluated associations between host age, host sex, and human population density and microbial community structure.ResultsThe cloacal microbiota included 29 phyla, 56 classes, and at least 131 orders, and was dominated by Bacillota, Actinomycetota, Pseudomonadota, and Bacteroidota. Common gutassociated taxa included Clostridium, Ruminococcus, and Eubacterium, whereas plant- and soil-associated bacteria, including nitrogen-fixing members of the Rhizobiaceae, likely reflect dietary and environmental acquisition during foraging. Alpha diversity metrics did not differ significantly across host age or sex, although ASV richness was significantly higher in rural compared to urban samples. In contrast, beta-diversity analyses indicated that host age was the strongest factor associated with differences in microbial community composition, with additional but weaker effects of human population density, while host sex had comparatively little influence. DiscussionOverall, these results suggest that ecological context, including habitat type and environmental exposure, were associated with variation in the cloacal microbiota of Canada goose, although additional unmeasured environmental and spatial factors may also contribute to observed patterns. This study provides a baseline characterization of microbiota variation across age classes and habitats in Illinois Canada goose and highlights the importance of considering ecological context when interpreting wildlife-associated microbial communities.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1904862</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1904862</link>
        <title><![CDATA[Correction: Fecal microbiota transplantation promotes gut microbiome recovery in pediatric hematopoietic stem cell transplant recipients]]></title>
        <pubdate>2026-06-17T00:00:00Z</pubdate>
        <category>Correction</category>
        <author>María Florencia Fernandez</author><author>Abigail Stricker</author><author>Adriana Bottero</author><author>Laura Busquet</author><author>Carlos Waldbaum</author><author>Fabiana López Mingorance</author><author>Raúl Martinez Patetta</author><author>Ignacio Toer</author><author>Ana Juliá</author><author>Andrea Mangano</author>
        <description></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1779816</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1779816</link>
        <title><![CDATA[Microbial community characterization of multi-crop growouts in the XROOTS aeroponic–hydroponic system on the International Space Station]]></title>
        <pubdate>2026-06-15T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Christina L. M. Khodadad</author><author>Cory J. Spern</author><author>Mary E. Hummerick</author><author>Jennifer L. Gooden</author><author>Cristiana J. Morales</author><author>Raymond M. Wheeler</author><author>Orlando Melendez</author><author>Robert Morrow</author><author>John Wetzel</author><author>Ye Zhang</author>
        <description><![CDATA[Plant growth systems tested on the International Space Station (ISS) are small-area growth units that mostly use solid media. With NASA’s plan to send astronauts on long-duration exploration missions, there is a need to produce larger amounts of fresh food with limited upmass and resources. The eXposed Root On-Orbit Test System (XROOTS) is an aeroponic–hydroponic nutrient delivery system designed for exploration missions and was tested on the ISS. Post-harvest samples were returned for microbiological analyses of the plant leaves, roots, and fruit from lettuce, mizuna mustard, wheat, radish, tomato, and pea plants grown in the XROOTS. The microbiological food safety of crops was evaluated through culture-based microbial enumeration and identification. The microbial communities were compared between different plants and plant tissues by sequencing the prokaryotic V4 variable region of the 16S ribosomal RNA (rRNA) gene amplicons and fungal internal transcribed spacer (ITS) region. The microbial counts from the root module surface samples demonstrated a reduction after cleansing. The bacterial counts in the nutrient solution ranged from 65 to 3,800 CFU/ml. The bacterial counts in the distal leaf sections were lower than those in the leaf proximal, wick, and roots in all plant samples. The tomato fruit and the pea pod samples had the lowest average counts. The microbial counts from the leaves and wicks harvested from XROOTS were similar to the ranges found on previous Veggie (Vegetable Production System)-grown leafy greens. All screening tests for potential foodborne pathogenic bacteria were negative. Sequencing analyses showed that diversity was low in the leaves and higher in the roots, and the microbial community was more diversified in the XROOTS samples compared with previous Veggie experiments. Pseudomonas had the highest relative abundance in the majority of samples. Although some microbes were shared in the majority of plant tissues, unique microbes were identified for each plant type grown in XROOTS and when compared with previous Veggie demonstrations. Microbial surveys of ISS-grown plants and the associated hardware provide valuable data that can reveal potential challenges in deep-space crop production operations and ensure the quality of crops intended for crew consumption.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1780965</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1780965</link>
        <title><![CDATA[Characterization of bacterial endophytes isolated from Cannabis sativa L. and Chelidonium majus L. for their application as biostimulants and biocontrol agents]]></title>
        <pubdate>2026-06-08T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mohammad Jamil Kaddoura</author><author>Laura Amaya-Quiroz</author><author>Mamta Rani</author><author>Zarna Shah</author><author>Kavya Reghunadh</author><author>Jamil Samsatly</author><author>Hacene Meglouli</author><author>Saji George</author>
        <description><![CDATA[Endophytic bacteria contribute to plant growth, stress tolerance, and pathogen resistance. Their effective use in agriculture requires the identification of strains that combine multiple beneficial traits with consistent performance across different field conditions. Accordingly, this study examines Bacillus and Pseudomonas endophytes isolated from Cannabis sativa L. and Chelidonium majus L. for plant growth promotion, abiotic stress tolerance, and biocontrol properties. Plant growth-promotion traits included indole, siderophore, and organic acid production, phosphate and zinc solubilization, and biofilm formation. Results showed that all the tested bacterial isolates produced indoles, with the highest levels recorded in Pseudomonas strain PPW-26, whereas several Pseudomonas strains exhibited strong siderophore production. Strain PPW-26 tested positive for methyl-red, indicating organic acid production, whereas other Pseudomonas strains tested negative. Moderate to high nutrient solubilization profiles were observed across all Pseudomonas strains. Bacillus strains, particularly BS-114, exhibited higher biofilm formation relative to Pseudomonas. Assessment of abiotic stress tolerance included proline accumulation, superoxide dismutase activity, and growth under varying temperature, salinity, and drought conditions. All strains displayed tolerance to the tested stresses, with Bacillus strains showing stronger resilience to high temperature and salinity, accompanied by elevated proline accumulation and superoxide dismutase activity in selected strains. Biocontrol potential was evaluated through biosurfactant production and antifungal activity. Bacillus strains showed high biosurfactant activity and strong inhibition of fungal pathogens. Strain BS-120 exhibited broad-spectrum inhibition against Fusarium oxysporum, Fusarium graminearum, and Rhizoctonia solani-AG3. Analysis of genome sequences identified biosynthetic gene clusters encoding antifungal metabolites, including fengycin and surfactin, consistent with the observed inhibition. Genome-wide similarity analysis and ANI-based clustering revealed the presence of highly similar and genetically distant strains within each genus. For Bacillus spp., ANI values ranged from 87.62% to 98.83%, whereas for Pseudomonas spp. they ranged between 83.91% and 99.99%, confirming the presence of substantial intra-genus diversity. Phylogenetic analysis showed well-supported clades consistent with ANI clustering. Overall, this study demonstrates that endophytic Bacillus and Pseudomonas strains exhibit complementary and strain-dependent traits associated with plant growth promotion, stress tolerance, and pathogen suppression, supporting their further evaluation as potential bioinoculants for sustainable agriculture.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1818652</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1818652</link>
        <title><![CDATA[Acute myocardial infarction induces sex-specific, time-dependent remodeling of the gut microbiome and intestinal immune compartment in retired breeder C57BL/6N mice]]></title>
        <pubdate>2026-06-08T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Eszter Pal</author><author>Neda Omidi Arjenaki</author><author>Yao Lu</author><author>Jianguo Xia</author><author>Lorraine Chalifour</author>
        <description><![CDATA[IntroductionThe gut microbiome influences cardiovascular health through metabolite production and immune modulation. Gut microbial dynamics and cardiovascular outcomes are also shaped by biological sex. However, sex-specific responses to myocardial infarction (MI) that involve the gut microbiome and intestinal milieu remain poorly defined, particularly in older hosts. Here, we characterize gut microbiome structure and function alongside physiological and immune responses to MI across multiple tissues in aging male and female mice.MethodsMI was induced by permanent LAD ligation and confirmed by echocardiography in C57BL/6N retired breeder mice. Sham surgery (SH) and no surgery (NoSx) groups served as controls. Gut microbiota and the cecal metabolome were characterized using 16S rRNA sequencing and untargeted UPLC-MS, respectively. Immune cells in the small intestine, heart, bone marrow, and spleen were quantified by flow cytometry, and small intestinal morphology was assessed on H&E-stained sections.ResultsSex-specific differences were evident at baseline. Following MI, pronounced time- and sex-specific differences in gut microbial and immune cell populations were observed, peaking on day 3 (D3) and absent in SH and NoSx controls. Early increases in Bacteroidaceae, Tannerellaceae, and Marinifilaceae were present in both sexes, with sex-specific enrichment of Bacteroidaceae in males and Akkermansiaceae in females. Metabolomic analyses identified increased secondary bile acid derivatives, including cholylvaline in males and 12-oxo-lithocholic acid in females. Integration of microbiota–metabolome data revealed MI-responsive and homeostatic taxa with opposing metabolite signatures, while functional analyses indicated enrichment of propanoate and amino acid metabolism pathways. These changes were temporally aligned with acute MI-induced expansion of intestinal MHCII+CD11c+ dendritic cells and TCRαβ+CD4+, TCRαβ+CD8αβ+, and CD25+FoxP3+ regulatory T cells on D3 in both sexes. Males alone exhibited marked increases in intestinal TCRγδ+ T cells, while females showed increased accumulation of innate immune cells.DiscussionConvergence of peak physiological, immunological, and microbial responses on day 3 after MI reveals coordinated responses across the gut-heart axis that are fundamentally influenced by sex. Our findings highlight the need for personalized, sex-specific perioperative strategies and identify the gut microbiome as a potential therapeutic target to improve outcomes after MI.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1639904</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1639904</link>
        <title><![CDATA[Exploring the gut–brain axis: dietary influences on Alzheimer’s disease pathogenesis]]></title>
        <pubdate>2026-06-08T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Samira R. Mansour</author><author>Menna A. Khalaf</author><author>Mostafa A. Moustafa</author><author>Mardies A. Moustafa</author><author>AbdelRaouf A. Moustafa</author>
        <description><![CDATA[Alzheimer’s disease (AD) is one of the most diagnosed neurodegenerative disorders worldwide and presents a significant challenge for both affected individuals and their caregivers. Alzheimer’s disease is characterized by the accumulation of amyloid plaques and dysfunctional tau protein in the brain, along with the final development of dementia. Recently, in addition to the strongly developing ischemic etiology of AD, it is suggested that the gut and oral microbiota may also participate in the development of this disease. This involvement may stem from an unbalanced diet and the consumption of foods containing harmful chemical additives. An unhealthy diet can compromise the integrity of the gut barrier, facilitating the translocation of bacterial pathogens and leading to a pro-inflammatory T-cell response mediated by innate immune cells. This inflammatory response can disrupt systemic homeostasis and may contribute to neuroinflammation. The brain and gut interact through a complex network known as the “gut–brain–microbiota axis,” and emerging studies suggest that the intestinal microbiota and their metabolites may play a significant role in the pathogenesis of Alzheimer’s disease. Moreover, these inflammatory mediators and microbial metabolites can reach the brain via the gut–brain axis, potentially exacerbating neurodegenerative processes. Preclinical and limited clinical evidence indicates that low-fiber diets are associated with alterations in intestinal microbiota composition, which may contribute to the onset and progression of Alzheimer’s disease. This review aims to explore the potential connections between AD and the gut microbiome, emphasizing the significance of dietary factors in shaping these relationships. A comprehensive understanding of the interactions between the human microbiome and the brain, particularly in the context of diet and its ingredients, may enhance our understanding of AD etiology and inform the development of preventative strategies, through dietary modifications or therapeutic interventions. This area of research holds promise for identifying novel approaches to prevent or slow the progression of AD.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1849762</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1849762</link>
        <title><![CDATA[Fecal microbiota transplantation promotes gut microbiome recovery in pediatric hematopoietic stem cell transplant recipients]]></title>
        <pubdate>2026-06-05T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>María Florencia Fernandez</author><author>Abigail Stricker</author><author>Adriana Bottero</author><author>Laura Busquet</author><author>Carlos Waldbaum</author><author>Fabiana López Mingorance</author><author>Raúl Martinez Patetta</author><author>Ignacio Toer</author><author>Ana Juliá</author><author>Andrea Mangano</author>
        <description><![CDATA[IntroductionHematopoietic stem cell transplantation (HSCT) profoundly disrupts the gut microbiome and may contribute to adverse post-transplant outcomes. Fecal microbiota transplantation (FMT) has emerged as a strategy to restore microbial diversity; however, data in pediatric HSCT recipients remain limited.MethodsWe conducted a longitudinal analysis of 17 pediatric HSCT recipients who received FMT. Fecal samples were collected before FMT and at days 7, 14, and 30 after treatment. Gut microbiome composition was analyzed using 16S rRNA gene sequencing.ResultsBaseline samples showed reduced microbial diversity and a dysbiotic microbial profile. Following FMT, microbial diversity increased progressively, with recovery evident from day 7 and stabilization by day 30. Taxonomic analyses demonstrated depletion of dysbiosis-associated genera and enrichment of beneficial short-chain fatty acid–producing taxa, including Faecalibacterium, Blautia, Subdoligranulum, and Akkermansia. Distinct microbial configurations were observed according to gastrointestinal involvement by acute graft-versus-host disease.ConclusionsFMT was associated with progressive restoration of gut microbiome diversity and structure in pediatric HSCT recipients, supporting its potential role as a microbiota-based strategy to promote ecological recovery after HSCT.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1785707</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1785707</link>
        <title><![CDATA[Altered early-life gut microbiota in offspring of pregnancies complicated by CHD-associated pulmonary hypertension]]></title>
        <pubdate>2026-05-29T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Yiyang Han</author><author>Haofeng Zhang</author><author>Jun Zhang</author>
        <description><![CDATA[BackgroundPulmonary arterial hypertension is a progressive disease involving the pulmonary vasculature and is defined as a mean pulmonary arterial pressure (mPAP) >20 mmHg at rest. Pulmonary arterial hypertension during pregnancy is associated with increased maternal mortality and adverse fetal outcomes. The present study aimed to investigate differences in the initial meconium microbiota between neonates born to mothers with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH) and those born to mothers with congenital heart disease (CHD) alone, thereby elucidating the potential influence of pulmonary arterial hypertension on the establishment of the early-life gut microbiome.MethodsWe collected first-pass meconium samples from neonates in the pulmonary hypertension group (PH group, n = 23) and the control group without pulmonary hypertension (NC group, n = 17) and characterized microbial profiles using 16S rRNA sequencing.ResultsThe PH group showed lower alpha diversity, with reduced Shannon and observed features indices (both P < 0.05), whereas Bray–Curtis beta diversity showed substantial overlap between groups. At the phylum level, the overall gut microbial structure was broadly comparable between the PH and NC groups, with no statistically significant differences in the relative abundance of dominant taxa. At the genus level, the mean relative abundance of Streptococcus was significantly lower in the PH group than in the NC group (0.20% vs. 2.09%, P = 0.0072). Predicted functional profiling suggested potential differences in dominant metabolic pathways between groups, including enrichment of ubiquinone biosynthesis and aromatic amino acid/chorismate biosynthesis pathways in the PH group.ConclusionCollectively, these findings extend current evidence on PAH-related alterations in early-life microbial ecosystems and provide a plausible microbiome-based basis for investigating the biological mechanisms underlying adverse maternal–fetal outcomes associated with pulmonary arterial hypertension.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1804117</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1804117</link>
        <title><![CDATA[Age-specific early-life gut microbiome associations with eczema and food allergies during early immune development]]></title>
        <pubdate>2026-05-29T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Harold Nunez</author><author>Timothy J. Straub</author><author>Nabeel Imam</author><author>David Goad</author><author>Noel T. Mueller</author><author>Ruben A. T. Mars</author><author>Cheryl Sew Hoy</author><author>Trillitye Paullin</author><author>Kimberley V. Sukhum</author>
        <description><![CDATA[IntroductionEczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.MethodsWe analyzed age-stratified shotgun metagenomic data from 97 children aged 4–36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4–6 months), mid-infancy (6–12 months), and toddlerhood (12–36 months).ResultsDifferences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.DiscussionThese findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1774429</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1774429</link>
        <title><![CDATA[The interplay between bile acid metabolism and gut microbiome in biliary tract cancers]]></title>
        <pubdate>2026-05-28T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Ifeoma Ike</author><author>Farzad Teymouri</author><author>Christiana Crook</author><author>Sofia Guzman</author><author>Max Hazeltine</author><author>Dani Castillo</author><author>Daneng Li</author><author>Gagandeep Brar</author>
        <description><![CDATA[The gut microbiota and bile acids (BAs) exist in a tightly regulated, bidirectional relationship that influences host metabolism, immune function, and disease. Primary BAs synthesized in the liver are chemically transformed by intestinal microbes into a diverse pool of secondary BAs, which exert antimicrobial effects and activate host signaling pathways including Farnesoid X Receptor (FXR), Takeda G protein–coupled receptor 5 (TGR5), and sphingosine-1-phosphate receptor 2 (S1PR2). These pathways regulate BA homeostasis, epithelial barrier integrity, inflammation, and carcinogenesis. Disruption of this BA–microbiome axis has been implicated in biliary tract cancers (BTCs), a group of aggressive malignancies with rising global incidence and limited therapeutic options. Secondary BAs and BA receptor signaling contribute to tumor initiation and progression through NF-κB activation, oxidative stress, and altered cell survival, whereas reduced FXR signaling and obstructed enterohepatic circulation further promote inflammatory dysregulation. Emerging evidence demonstrates that microbial dysbiosis and altered BA metabolism are associated with distinct BTC microbial profiles, enriched in taxa such as Fusobacterium, Salmonella, Prevotella, and Actinomyces, alongside depletion of commensals including Lactobacillus. These taxa influence inflammatory signaling, BA transformation, and epithelial injury, contributing to carcinogenesis. Microbiome–BA interactions also shape anti-tumor immunity and responses to immune checkpoint inhibitors (ICIs). Specific microbial signatures—particularly enrichment of Lachnospiraceae, Erysipelotrichaceae, Bacteroidetes, and Alistipes—correlate with enhanced immune activation and improved clinical outcomes in hepatobiliary cancers. Modulation of gut microbiota through antibiotics, probiotics, or fecal microbiota transplantation can influence BA composition, immune surveillance, and therapeutic efficacy. Collectively, these data highlight the central role of the BA–microbiome axis in BTC pathogenesis and treatment response. Microbial and BA metabolite profiling represent promising avenues for biomarker development, while targeted manipulation of BA signaling and microbial ecology offers potential therapeutic strategies to improve BTC outcomes.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1808609</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1808609</link>
        <title><![CDATA[Soil microbial communities shift in response to cropping sequence diversification with perennial seed crops]]></title>
        <pubdate>2026-05-26T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Newton Z. Lupwayi</author><author>Nityananda Khanal</author><author>Mathew Richards</author><author>Rodrigo Ortega Polo</author>
        <description><![CDATA[Integrating perennial forage seed crops into annual cropping sequences can diversify the rotations and improve soil health, yet their effects on the soil microbial communities and functions are not yet fully elucidated on the Canadian prairies. Using a 10-year field experiment with eight cropping sequences under varying supplemental nitrogen (N) fertilization levels, we evaluated the impacts of integrating perennial seed crops and annual crops on soil microbial biomass carbon (MBC), the composition and diversity of prokaryotic and fungal communities, and the activities of key enzymes involved in carbon (C), N, phosphorus (P), and sulfur (S) cycling, namely β-glucosidase, N-acetyl-β-glucosaminidase, acid phosphomonoesterase and arylsulfatase. The crop sequences containing intermittent succession of perennial and annual crops had 17% greater soil MBC, higher fungal richness (e.g., Chao1 indices of 92.8 vs. 87.6) and 22% greater β-glucosidase activity than annual-only sequences. The relative abundances of the two most abundant prokaryotic phyla - Actinobacteriota and Proteobacteria - as well as the second most abundant fungal class, Dothideomycetes, followed the same trend. The soils with more frequent recurrence of grassy perennials in the sequences exhibited greater MBC (34%), higher prokaryotic Shannon diversity, greater fungal richness, and higher arylsulfatase activity (68%) than soils with more frequent recurrence of perennial legumes, although the predominant prokaryotic phylum, Actinobacteriota was more abundant in legume-based systems. The cropping sequences dominated by creeping red fescue grass seed crops exhibited the greatest improvement in most of the soil microbial metrics studied. Nitrogen fertilizer increased the relative abundance of the copiotrophic Actinobacteriota but decreased that of the oligotrophic Acidobacteriota. Prokaryotes were associated with C, N, P and S cycling, whereas fungi were primarily linked to C cycling. Overall, diversifying annual grain cropping systems with perennial forage seed crops, particularly creeping red fescue, enhanced key indicators of biological soil health.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1832705</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1832705</link>
        <title><![CDATA[Dietary transition to an Indigenous Greenlandic diet induces instant shifts in gut microbiota composition – a pilot intervention study]]></title>
        <pubdate>2026-05-21T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Mads B. W. Bjørnsen</author><author>Katie M. Bourke</author><author>Catherine Stanton</author><author>R. Paul Ross</author><author>Anders J. Hansen</author><author>Aviaja L. Hauptmann</author>
        <description><![CDATA[IntroductionNon-Western diets are increasingly studied for their relationship to gut microbiota composition and diversity, although most research in this area has focused on plant-based, fiber-rich diets. Here, we present a single-participant longitudinal study investigating gut microbiota dynamics during a transition from a Western diet to a 12-week Indigenous Arctic animal-based diet composed of minimally processed raw, dried, and fermented animal-source foods. During one month of this period, the participant consumed dried whole fish (ammassak), including intestinal contents, representing a form of gastrophagy, a practice common to the Arctic diet, that may increase exposure to food-associated microbes.MethodsFecal samples (n = 29) were collected before, during, and after the Arctic diet phase. 16S rRNA gene sequencing of the V3-V4 region was used to profile bacterial communities. Diversity metrics, Firmicutes/Bacteroidota (F/B) ratios, and taxonomic composition analyses were performed to assess compositional shifts across diet phases.ResultsAlpha diversity remained relatively steady throughout the study, with a tendency toward higher values during the Arctic diet. The F/B ratio increased from 1.31 to 2.12 during the Arctic diet phase and remained elevated (2.38) after returning to a Western diet. Beta diversity analysis revealed significant restructuring of the gut microbiota at the onset of the Arctic diet, followed by partial reversibility upon returning to a Western diet. Fiber-associated taxa like Prevotella 9 disappeared, and Bifidobacterium declined, while protein- and fat-associated taxa, including Bacteroides, Lachnoclostridium, and Alistipes, increased. Several genera appeared during the Arctic diet phase that were absent during the preceding Western diet phase, consistent with altered microbial exposure. Among those, Photobacterium was also detected in the ammassak, suggesting potential microbial exposure during the gastrophagy period.DiscussionThese results provide preliminary evidence that the gut microbiota can shift substantially during an Indigenous Arctic dietary transition. Because the Arctic diet also substantially overlapped with sustained high physical activity, the observed changes should be interpreted in the context of a combined dietary and lifestyle transition. These findings highlight the need for a better understanding of underrepresented dietary patterns, such as those of Arctic Indigenous communities, and their relationship with the gut microbiota.]]></description>
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        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1778537</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1778537</link>
        <title><![CDATA[Host genotype and environment shape rhizosphere and root microbiome composition of pecan rootstocks]]></title>
        <pubdate>2026-05-15T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Paul Oladimeji Gabriel</author><author>Ciro Velasco-Cruz</author><author>Jennifer J. Randall</author>
        <description><![CDATA[The rhizosphere and root-associated microbiomes play a crucial role in nutrient acquisition, stress tolerance, and overall plant performance. However, little is known about how microbial communities assemble and shift across environments in pecan (Carya illinoinensis). In this study, we compared the bacterial and fungal community compositions in the roots and rhizosphere of four pecan clonal rootstocks (NMU03, NMU04, NMU05, and NMU155) cultivated under greenhouse conditions, as well as their subsets that were subsequently transplanted to the field. Amplicon sequencing of 16S rRNA and ITS regions revealed significant differences in microbial diversity and taxonomic composition across environments and genotypes. Bacterial assemblages in greenhouse roots were typically dominated by a few families (e.g., Burkholderiaceae, Rhodanobacteraceae, and unclassified taxa). In contrast, field samples exhibited broader taxonomic distributions, with families such as Xanthobacteraceae, Haliangiaceae, and Geminicoccaceae emerging as dominant members. Fungal OTU abundance was consistently higher than bacterial abundance across all genotypes, likely reflecting mutualistic associations with mycorrhizal fungi, such as those in the Elaphomycetaceae family. Interestingly, Aspergillaceae dominated greenhouse and field fungal communities, suggesting ecological adaptability and potential contributions to plant stress tolerance. Comparisons with earlier greenhouse studies revealed that while some signature core microbiome members were retained following transplantation from the greenhouse to the field, the abundance of others decreased, highlighting successional shifts in community structure driven by environmental transitions. Together, these findings demonstrate the dynamic, genotype and environment-specific structuring of pecan microbiomes and highlight the importance of microbiome-informed breeding strategies to improve plant-microbe associations under variable growth conditions among pecan breeders.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1842701</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1842701</link>
        <title><![CDATA[Computational and multi-omics systems biology for precision microbiome therapeutics]]></title>
        <pubdate>2026-05-15T00:00:00Z</pubdate>
        <category>Mini Review</category>
        <author>Ahmed Dewan</author><author>Maria Teresa Mascellino</author>
        <description><![CDATA[The human gut microbiome represents a complex and dynamic therapeutic target whose effective interrogation requires system-level analytical approaches beyond single-omics or reductive methods. This mini-review synthesizes recent advances in computational modeling and multi-omics integration relevant to the development of predictive, patient-tailored microbiome therapies. We critically assess the analytical strengths and limitations of genome-scale metabolic models (GEMs); generalized Lotka–Volterra and ODE-based community models; agent-based simulations; and statistical machine-learning frameworks and examine how their integration with metagenomics, metatranscriptomics, metaproteomics, and metabolomics can help bridge microbial functional potential with clinically relevant phenotypes. Representative applications–including MintTea for disease module identification, gNOMO2 for integrative microbiome profiling, and AGORA-based community metabolic modeling–illustrate the translational scope of these frameworks across inflammatory, metabolic, and infectious disease contexts. Hybrid ML–GEM frameworks have not yet been directly applied to FMT outcome prediction; however, the mechanistic principles underlying both approaches – metabolic compatibility modeling and data-driven responder stratification – suggest a compelling direction for future investigation, contingent on prospective validation in adequately powered and independent clinical cohorts. Persistent methodological challenges–such as data heterogeneity, batch effects across sequencing platforms, incomplete multi-omics coverage, and limited interpretability of complex machine-learning models–are being actively addressed through standardized preprocessing pipelines, explainable Artificial intelligence (AI) strategies, and federated analytics. While federated approaches enable privacy-preserving, multi-institutional model training, they introduce additional constraints related to non-identically distributed data, communication overhead, and uneven computational capacity. Overall, the convergence of mechanistic modeling, data-driven learning, and distributed analytical infrastructures may assist in advancing microbiome research from a largely correlational perspective toward mechanistic and ultimately prescriptive frameworks for precision microbiome medicine.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1803341</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1803341</link>
        <title><![CDATA[Protist community sites and structure under two barn management systems at a commercial dairy]]></title>
        <pubdate>2026-05-14T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Tawni L. Crippen</author><author>Dongmin Kim</author><author>Sonja L. Swiger</author><author>Robin C. Anderson</author>
        <description><![CDATA[IntroductionInvestigations into the location and load of protists in the environment arounddairies are scarce but are essential to maintaining the health of livestock.Moreover, the design of dairy barns has fluctuated over the decades to maximizecattle health and milk production without regard to influences on environmentalmicrobiomes. Beyond cost, the major emphasis of barn design is the managementof appropriate temperature and comfort for cattle. However, there havebeen no corresponding investigations into whether these design changes affect protist communities within barns.MethodsIn this study, community shotgun metagenomic analysis was used to define the spatial composition and relative abundance of protist communities from 118 samples of manure, lagoons, troughs, and house and stable flies at a commercial dairy implementing two free-stall management systems: flow-through and cross-vent. Sequence reads were mapped to the CosmosID database. Viability was not assessed; therefore, results reflect DNA detection only not viability or disease occurrence.ResultsThe protist composition differed significantly between dairy components. Ecological findings showed that troughs and lagoons harbored high protist diversity, including the possible pathogen Neobalantidium coli and potential carriers Paramecium biaurelia and Acanthamoeba. Manure had the lowest protist diversity. Stable flies carried more protist taxa than house flies. Both fly species uniquely carried the non-pathogenic alveolate parasite Hammondia hammondi. The water mold plant pathogen Pseudoperonospora cubensis was identified in all sample types. Of the total relative abundance of protists, 2.10% were amoebas, 7.63% alveolate parasites, 62.71% water molds, 23.31% ciliates, 1.74% foraminifera, and 2.50% diatoms.DiscussionThese results describe preliminary spatial overlaps and possible avenues of dissemination, providing a basis for assessing appropriate management systems and identifying protist reservoir sites within dairy operations.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1831956</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1831956</link>
        <title><![CDATA[Identifying microbial biomarkers of neurodegeneration: a comparative study in Alzheimer’s and Parkinson’s disease]]></title>
        <pubdate>2026-05-12T00:00:00Z</pubdate>
        <category>Original Research</category>
        <author>Simon De Jaegher</author><author>David Pinzauti</author><author>Maria D’Aguanno</author><author>Erika Parkinson</author><author>James Schofield</author><author>Fabio Strazzeri</author><author>Paul Skipp</author><author>Rebekah Penrice-Randal</author><author>Amy Kunicki</author><author>Beth McCausland</author><author>Christopher Kipps</author><author>Jay Amin</author><author>Manuele Biazzo</author>
        <description><![CDATA[IntroductionNeurodegenerative disorders such as Alzheimer’s disease (AD) and Parkinson’s disease (PD) have been increasingly linked to alterations of the gut microbiota, although reported microbial signatures remain heterogeneous and often lack taxonomic resolution.MethodsIn the present study, we applied full-length 16S rRNA gene sequencing to characterize gut microbiota composition in 152 individuals, including patients with AD (n = 37), PD (n = 65), and age-matched healthy controls (n = 50), using a unified bioinformatic and statistical framework with adjustment for relevant demographic covariates.ResultsAlzheimer’s disease was associated with a modest but significant reduction in microbial richness and Shannon diversity compared with controls, whereas no alpha diversity differences were observed in PD. Beta diversity analyses revealed significant compositional differences across diagnostic groups, driven primarily by PD and modulated by sex but not age. Species-level differential abundance analysis identified a PD-associated microbial signature characterized by reduced abundances of short-chain fatty acid-producing bacteria, including Faecalibacterium prausnitzii, Agathobacter rectalis, Roseburia intestinalis, and Faecalicatena fissicatena, together with increased abundance of Ruminococcus sp. JE7A12. In contrast, AD exhibited minimal species-level changes, with only Bacteroidales bacterium CF showing reduced abundance compared with controls.DiscussionOverall, these findings indicate that Parkinson’s disease is characterized by a targeted disruption of beneficial butyrate-producing bacteria, whereas Alzheimer’s disease exhibits subtler and less consistent microbiome alterations. Our results underscore the importance of species-level resolution for identifying disease-associated microbial signatures.]]></description>
      </item><item>
        <guid isPermaLink="true">https://www.frontiersin.org/articles/10.3389/frmbi.2026.1787662</guid>
        <link>https://www.frontiersin.org/articles/10.3389/frmbi.2026.1787662</link>
        <title><![CDATA[Importance of human microbiome: an update]]></title>
        <pubdate>2026-04-30T00:00:00Z</pubdate>
        <category>Review</category>
        <author>Maryem Wardi</author><author>Abdulmumini Baba Amin</author><author>Imane El Belghiti</author><author>Zohra Lemkhente</author><author>Ahmed Belmouden</author>
        <description><![CDATA[Millions of microorganisms—including bacteria, viruses, fungi, archaea, and protists—reside on and within the human body, collectively forming the human microbiota. This complex and dynamic community plays a crucial role in modulating physiological processes, particularly the development and regulation of the immune system. Modern behaviors such as frequent washing, excessive hygiene, and widespread use of antimicrobial agents can disrupt the natural composition and functional balance of the microbiota, leading to altered immune responses and increased susceptibility to disease. In this review, we focus primarily on the bacterial component of the human microbiome. While we acknowledge the importance of viruses, fungi, archaea, and protists, these components are beyond the scope of the current review. We highlight recent advances in bacterial microbiome research that are reshaping our understanding of host–microbe interactions, immune modulation, and the health consequences of microbiota dysbiosis.]]></description>
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