Microbiome最新文献

{"title":"Distinct gut microbiome characteristics and dynamics in patients with Parkinson's disease based on the presence of premotor rapid-eye movement sleep behavior disorders.","authors":"Jae-Yun Lee, Sungyang Jo, Jihyun Lee, Moongwan Choi, Kijeong Kim, Sangjin Lee, Hyun Sik Kim, Jin-Woo Bae, Sun Ju Chung","doi":"10.1186/s40168-025-02095-w","DOIUrl":"https://doi.org/10.1186/s40168-025-02095-w","url":null,"abstract":"<p><strong>Background: </strong>Alpha-synuclein aggregation, a hallmark of Parkinson's disease (PD), is hypothesized to often begin in the enteric or peripheral nervous system in \"body-first\" PD and progresses through the vagus nerve to the brain, therefore REM sleep behavior disorder (RBD) precedes the PD diagnosis. In contrast, \"brain-first\" PD begins in the central nervous system. Evidence that gut microbiome imbalances observed in PD and idiopathic RBD exhibit similar trends supports body-first and brain-first hypothesis and highlights the role of microbiota in PD pathogenesis. However, further investigation is needed to understand distinct microbiome changes in body-first versus brain-first PD over the disease progression.</p><p><strong>Results: </strong>Our investigation involved 104 patients with PD and 85 of their spouses as healthy controls (HC), with 57 patients (54.8%) categorized as PD-RBD(+) and 47 patients (45.2%) as PD-RBD(-) based on RBD presence before the PD diagnosis. We evaluated the microbiome differences between these groups over the disease progression through taxonomic and functional differential abundance analyses and carbohydrate-active enzyme (CAZyme) profiles based on metagenome-assembled genomes. The PD-RBD(+) gut microbiome showed a relatively stable microbiome composition irrespective of disease stage. In contrast, PD-RBD(-) microbiome exhibited a relatively dynamic microbiome change as the disease progressed. In early-stage PD-RBD(+), Escherichia and Akkermansia, associated with pathogenic biofilm formation and host mucin degradation, respectively, were enriched, which was supported by functional analysis. We discovered that genes of the UDP-GlcNAc synthesis/recycling pathway negatively correlated with biofilm formation; this finding was further validated in a separate cohort. Furthermore, fiber intake-associated taxa were decreased in early-stage PD-RBD(+) and the biased mucin-degrading capacity of CAZyme compared to fiber degradation.</p><p><strong>Conclusion: </strong>We determined that the gut microbiome dynamics in patients with PD according to the disease progression depend on the presence of premotor RBD. Notably, early-stage PD-RBD(+) demonstrated distinct gut microbial characteristics, potentially contributing to exacerbation of PD pathophysiology. This outcome may contribute to the development of new therapeutic strategies targeting the gut microbiome in PD. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"108"},"PeriodicalIF":13.8,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042535/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143970502","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Quantitative stable isotope probing (qSIP) and cross-domain networks reveal bacterial-fungal interactions in the hyphosphere.","authors":"Giovana S Slanzon, Mengting Yuan, Katerina Estera-Molina, Aaron Chew, Steve J Blazewicz, Michael Allen, Mary K Firestone, Jennifer Pett-Ridge, Nhu H Nguyen","doi":"10.1186/s40168-025-02100-2","DOIUrl":"https://doi.org/10.1186/s40168-025-02100-2","url":null,"abstract":"<p><strong>Background: </strong>Interactions between fungi and bacteria have the potential to substantially influence soil carbon dynamics in soil, but we have yet to fully identify these interactions and partners in their natural environment. In this study, we stacked two powerful methods, ¹³C quantitative stable isotope probing (qSIP) and cross-domain co-occurrence network, to identify interacting fungi and bacteria in a California grassland soil. We used in-field whole plant ¹³CO₂ labeling along with sand-filled ingrowth bags (that trap fungi and hyphae-associated bacteria) to amplify the signal of fungal-bacterial interactions, separate from the bulk soil background.</p><p><strong>Results: </strong>We found a total of 54 bacterial ASVs and 9 fungal OTUs that were significantly ¹³C-enriched. These were saprotrophic and biotrophic fungi, and motile, sometimes predatory bacteria. Among these, 70% of all ¹³C-enriched bacteria identified were motile. Notably, we detected fungal-bacterial network links between a fungal OTU of the genus Alternaria and several bacterial ASVs of the genera Bacteriovorax, Mucilaginibacter, and Flavobacterium, providing empirical evidence of their direct interactions through C exchange. We observed a strong positive co-occurrence pattern between predatory bacteria of the phylum Bdellovibrionota and fungal OTUs, suggesting the transfer of C across the soil food web.</p><p><strong>Conclusions: </strong>To date, our ability to associate microbial co-occurrence network patterns with biological interactions is limited, but the incorporation of qSIP allowed us to more precisely detect interacting partners by narrowing in on the taxa that were actively incorporating plant-fixed, fungal-transported labeled substrates. Together, these approaches can help build a mechanistic understanding of the complex nature of fungal-bacterial interactions in soil.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"109"},"PeriodicalIF":13.8,"publicationDate":"2025-04-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12044819/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144009209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bikaverin as a molecular weapon: enhancing Fusarium oxysporum pathogenicity in bananas via rhizosphere microbiome manipulation.","authors":"Honglin Lu, Suxia Guo, Yongbao Yang, Zhihao Zhao, Qingbiao Xie, Qiong Wu, Changjun Sun, Hongli Luo, Bang An, Qiannan Wang","doi":"10.1186/s40168-025-02109-7","DOIUrl":"https://doi.org/10.1186/s40168-025-02109-7","url":null,"abstract":"<p><strong>Background: </strong>Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), poses a severe threat to global banana production. Secondary metabolites are critical tools employed by pathogens to interact with their environment and modulate host-pathogen dynamics. Bikaverin, a red-colored polyketide pigment produced by several Fusarium species, has been studied for its pharmacological properties, but its ecological roles and impact on pathogenicity remain unclear.</p><p><strong>Results: </strong>This study investigated the role of bikaverin in Foc TR4, focusing on its contribution to pathogenicity and its interaction with the rhizosphere microbiome. Pathogenicity assays under sterile and autoclaved conditions demonstrated that bikaverin does not directly contribute to pathogenicity by affecting the infection process or damaging host tissues. Instead, bikaverin indirectly enhances Foc TR4's pathogenicity by reshaping the rhizosphere microbiome. It suppresses beneficial plant growth-promoting rhizobacteria, such as Bacillus, while promoting the dominance of fungal genera, thereby creating a microbial environment beneficial for pathogen colonization and infection. Notably, bikaverin biosynthesis was found to be tightly regulated by environmental cues, including acidic pH, nitrogen scarcity, and microbial competition. Co-culture with microbes such as Bacillus velezensis and Botrytis cinerea strongly induced bikaverin production and upregulated expression of the key bikaverin biosynthetic gene FocBik1. In addition, the identification of bikaverin-resistant Bacillus BR160, a strain with broad-spectrum antifungal activity, highlights its potential as a biocontrol agent for banana wilt management, although its stability and efficiency under field conditions require further validation.</p><p><strong>Conclusions: </strong>Bikaverin plays an indirect yet important role in the pathogenicity of Foc TR4 by manipulating the rhizosphere microbiome. This ecological function underscores its potential as a target for sustainable disease management strategies. Future research should focus on elucidating the molecular mechanisms underlying bikaverin-mediated microbial interactions, using integrated approaches such as transcriptomics and metabolomics. Together, these findings provide a foundation for novel approaches to combat banana wilt disease and enhance crop resistance. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"107"},"PeriodicalIF":13.8,"publicationDate":"2025-04-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042607/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007304","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modest functional diversity decline and pronounced composition shifts of microbial communities in a mixed waste-contaminated aquifer.","authors":"Yupeng Fan, Dongyu Wang, Joy X Yang, Daliang Ning, Zhili He, Ping Zhang, Andrea M Rocha, Naijia Xiao, Jonathan P Michael, Katie F Walker, Dominique C Joyner, Chongle Pan, Michael W W Adams, Matthew W Fields, Eric J Alm, David A Stahl, Terry C Hazen, Paul D Adams, Adam P Arkin, Jizhong Zhou","doi":"10.1186/s40168-025-02105-x","DOIUrl":"https://doi.org/10.1186/s40168-025-02105-x","url":null,"abstract":"<p><strong>Background: </strong>Microbial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated microbial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (< 3).</p><p><strong>Results: </strong>Both taxonomic and phylogenetic α-diversities were reduced in the most impacted wells, while the decline in functional α-diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional β-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy.</p><p><strong>Conclusions: </strong>Overall, we demonstrated that despite a reduced taxonomic α-diversity, microbial communities under stress maintained functionality underpinned by environmental selection. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"106"},"PeriodicalIF":13.8,"publicationDate":"2025-04-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12036129/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144031563","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Soybean productivity can be enhanced by understanding rhizosphere microbiota: evidence from metagenomics analysis from diverse agroecosystems.","authors":"Honglei Ren, Huilong Hong, Bire Zha, Sobhi F Lamlom, Hongmei Qiu, Yongqiang Cao, Rujian Sun, Haorang Wang, Junkui Ma, Hengbin Zhang, Liping Sun, Qing Yang, Changjun Zhou, Xiulin Liu, Xueyang Wang, Chunlei Zhang, Fengyi Zhang, Kezhen Zhao, Rongqiang Yuan, Ahmed M Abdelghany, Bixian Zhang, Yuhong Zheng, Jiajun Wang, Wencheng Lu","doi":"10.1186/s40168-025-02104-y","DOIUrl":"https://doi.org/10.1186/s40168-025-02104-y","url":null,"abstract":"<p><strong>Background: </strong>Microbial communities associated with roots play a crucial role in the growth and health of plants and are constantly influenced by plant development and alterations in the soil environment. Despite extensive rhizosphere microbiome research, studies examining multi-kingdom microbial variation across large-scale agricultural gradients remain limited.</p><p><strong>Results: </strong>This study investigates the rhizosphere microbial communities associated with soybean across 13 diverse geographical locations in China. Using high-throughput shotgun metagenomic sequencing on the BGISEQ T7 platform with 10 GB per sample, we identified a total of 43,337 microbial species encompassing bacteria, archaea, fungi, and viruses. Our analysis revealed significant site-specific variations in microbial diversity and community composition, underscoring the influence of local environmental factors on microbial ecology. Principal coordinate analysis (PCoA) indicated distinct clustering patterns of microbial communities, reflecting the unique environmental conditions and agricultural practices of each location. Network analysis identified 556 hub microbial taxa significantly correlated with soybean yield traits, with bacteria showing the strongest associations. These key microorganisms were found to be involved in critical nutrient cycling pathways, particularly in carbon oxidation, nitrogen fixation, phosphorus solubilization, and sulfur metabolism. Our findings demonstrate the pivotal roles of specific microbial taxa in enhancing nutrient cycling, promoting plant health, and improving soybean yield, with significant positive correlations (r = 0.5, p = 0.039) between microbial diversity and seed yield.</p><p><strong>Conclusion: </strong>This study provides a comprehensive understanding of the diversity and functional potential of rhizosphere microbiota in enhancing soybean productivity. The findings underscore the importance of integrating microbial community dynamics into crop management strategies to optimize nutrient cycling, plant health, and yield. While this study identifies key microbial taxa with potential functional roles, future research should focus on isolating and validating these microorganisms for their bioremediation and biofertilization activities under field conditions. This will provide actionable insights for developing microbial-based agricultural interventions to improve crop resilience and sustainability. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"105"},"PeriodicalIF":13.8,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12034204/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143971500","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Viral activity in lake analogs of anoxic early Earth oceans.","authors":"Natascha S Varona, Bailey A Wallace, Alice Bosco-Santos, Julianna Mullinax, Alexandra K Stiffler, Molly D O'Beirne, Josh Ford, James M Fulton, Josef P Werne, William P Gilhooly, Cynthia B Silveira","doi":"10.1186/s40168-025-02085-y","DOIUrl":"https://doi.org/10.1186/s40168-025-02085-y","url":null,"abstract":"<p><strong>Background: </strong>Meromictic lakes, with their stratified water columns, are modern analogs for ancient euxinic (anoxic and sulfidic) oceans, where anaerobic sulfur-oxidizing purple and green sulfur bacteria (PSB and GSB) dominated as primary producers. Recent studies suggest a potential role of viruses in the metabolisms and biosignatures of these bacteria, but conclusive evidence of viral replication and activity in such lakes is still lacking.</p><p><strong>Results: </strong>Here, we investigate viral activity in the upper mixed layer (mixolimnion), the anoxic bottom (monimolimnion), and the microbial plate (a dense layer of phototrophic sulfur bacteria forming at the boundary between the oxygenated mixolimnion and the anoxic monimolimnion) of three meromictic lakes: Poison and Lime Blue Lakes (WA, USA) and Mahoney Lake (BC, CA). Geochemical profiles of two lakes, Mahoney and Poison, which are dominated by PSB, show a sharp chemocline, whereas Lime Blue displays a less steep chemical gradient and hosts a mixture of PSB and GSB. Viral gene transcription and epifluorescence microscopy revealed depth-dependent patterns in viral activity. The two strongly stratified, PSB-dominated lakes showed a significant decrease in the virus-to-microbe ratio (VMR) in their microbial plates, suggesting reduced viral particle production via lysis. Metatranscriptome data corroborated this trend by showing lower levels of viral gene expression in these microbial plates, higher expression of CRISPR defense and lysogeny-related genes, and relatively high expression of photosynthesis-related viral genes. Conversely, the third lake, which harbors a mix of PSB and GSB, exhibited low microbial density, high VMR, and high viral transcriptional activity. Viral transcription levels significantly correlated with VMR in the microbial plates and bottom layers, but this relationship was absent in low-density, oxic surface samples.</p><p><strong>Conclusions: </strong>Here, two independent lines of evidence, abundances and gene expression, show reduced viral lytic production in microbial plates dominated by PSB in stratified lakes. This suggests that viral lysis may contribute less to bacterial community structuring in these high-density microbial plates. Rather, other viral-mediated mechanisms, such as lysogeny and the expression of auxiliary metabolic genes, may represent a more significant viral influence on bacterial physiology and geochemistry. These patterns in virus-bacteria interactions may be consequential for the interpretations of biosignatures left by these bacterial groups in the geologic record. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"104"},"PeriodicalIF":13.8,"publicationDate":"2025-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12032784/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144033576","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Enhanced propionate and butyrate metabolism in cecal microbiota contributes to cold-stress adaptation in sheep.","authors":"Xindong Cheng, Yanping Liang, Kaixi Ji, Mengyu Feng, Xia Du, Dan Jiao, Xiukun Wu, Chongyue Zhong, Haitao Cong, Guo Yang","doi":"10.1186/s40168-025-02096-9","DOIUrl":"https://doi.org/10.1186/s40168-025-02096-9","url":null,"abstract":"&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;During cold stress, gut microbes play crucial roles in orchestrating energy metabolism to enhance environmental adaptation. In sheep, hindgut microbes ferment carbohydrates to generate short-chain fatty acids (SCFAs) as an energy source. However, the mechanisms by which hindgut microbes and their metabolites interact with the host to facilitate adaptation to cold environments remain ambiguous. Herein, we simulated a winter environment (- 20 °C) and provided a rationed diet to compare the cold adaptation mechanisms between Hulunbuir and Hu sheep.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;Our findings show that cold exposure enhances SCFA metabolism in the sheep cecum. In Hu sheep, acetate, butyrate, and total SCFA concentrations increased, whereas in Hulunbuir sheep, propionate and butyrate concentrations increased, with a notable increase in total SCFAs. Notably, butyrate concentration was higher in Hulunbuir sheep than in Hu sheep under cold stress. Following cold exposure, the proinflammatory cytokine IL-1β levels increased in both breeds. In addition, Hu sheep showed increased IL-10, whereas Hulunbuir sheep exhibited elevated secretory IgA levels. The cecal microbiota responded differently, Hu sheep showed no notable changes in alpha and beta diversity, whereas Hulunbuir sheep exhibited considerable alterations. In Hu sheep, the abundance of fungi, specifically Blastocystis sp. subtype 4, decreased, and that of several Lachnospiraceae species (Roseburia hominis, Faecalicatena contorta, and Ruminococcus gnavus) involved in SCFA metabolism increased. Pathways related to carbohydrate metabolism, such as starch and sucrose metabolism, galactose metabolism, and pentose and glucuronate interconversions, were upregulated. In Hulunbuir sheep, the abundance of Treponema bryantii, Roseburia sp. 499, and Prevotella copri increased, with upregulation in pathways related to amino acid metabolism and energy metabolism. Cold exposure increased node connectivity within the symbiotic networks of both breeds, with increased network vulnerability in Hu sheep. Following cold exposure, the microbial community of Hulunbuir sheep showed a decrease in the influence of stochastic processes on community assembly, with a corresponding increase in the role of environmental selection. Conversely, no such shift was evident in Hu sheep. Further transcriptomic analysis revealed distinct regulatory mechanisms between breeds. In Hu sheep, protein synthesis, energy metabolism, and thermogenesis pathways were substantially upregulated. By contrast, Hulunbuir sheep showed considerable upregulation of immune pathways and energy conservation through reduced ribosome synthesis. Correlation analysis indicated that butyrate holds a central position in both networks, with Hulunbuir sheep exhibiting a more complex and tightly regulated network involving SCFAs, microbiota, microbial functions, and transcriptomes. Partial least squares path modeling revealed that col","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"103"},"PeriodicalIF":13.8,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12023611/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016008","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deterministic colonization arises early during the transition of soil bacteria to the phyllosphere and is shaped by plant-microbe interactions.","authors":"Teresa Mayer, Erik Teutloff, Kerstin Unger, Pamela Lehenberger, Matthew T Agler","doi":"10.1186/s40168-025-02090-1","DOIUrl":"https://doi.org/10.1186/s40168-025-02090-1","url":null,"abstract":"<p><strong>Background: </strong>Upon seed germination, soil bacteria are activated to transition to the plant and eventually colonize mature tissues like leaves. These bacteria are poised to significantly influence plant health, but we know little about their colonization routes. We studied the mechanisms of the transition of soil bacteria to germinating plants and leaves using an in-planta isolation approach and by experimentally manipulating inoculation times. We then tested how plant-microbe-microbe interactions shape assembly mechanisms in natural soil communities by amending soil with a trackable, labeled strain of the opportunistic pathogen Pseudomonas viridiflava (Pv3D9).</p><p><strong>Results: </strong>We identified 27 diverse genera of leaf-associated bacteria that could transition alone from a few cells near a germinating plant to mature leaves, suggesting that the soil-to-leaf transition is probably important for them in nature. Indeed, when plants were only inoculated by soil after the emergence of true leaves, less diverse bacteria transitioned to mature leaves via different colonization mechanisms than when plants germinated in the presence of soil microorganisms. In particular, deterministic processes drove the colonization of phylogenetic bins dominated by Pedobacter, Enterobacter, Stenotrophomonas, Janthinobacterium, Pseudomonas, and Chryseobacterium only in the natural soil-to-leaf transition. Host genotype and soil amendments with Pv3D9, both of which affect host physiology, had strong effects on mainly deterministic colonization.</p><p><strong>Conclusions: </strong>Diverse bacteria transition from soil to leaves during natural colonization, resulting in characteristic diversity in healthy leaf microbiomes. The mechanisms of colonization are a mix of stochastic processes, which will be largely shaped by competition, and deterministic processes which are more responsive to factors that shape host physiology. In the chase toward targeted manipulation of microbiomes, identifying these mechanisms for a given host and environment provides important information. Developing targeted treatments, however, will require further dissection of the pathways by which host factors drive stochastic and deterministic transitions from soil to leaves. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"102"},"PeriodicalIF":13.8,"publicationDate":"2025-04-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12013066/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model.","authors":"Thibault Cuisiniere, Roy Hajjar, Manon Oliero, Annie Calvé, Gabriela Fragoso, Hervé Vennin Rendos, Claire Gerkins, Nassima Taleb, Marianne Gagnon-Konamna, François Dagbert, Rasmy Loungnarath, Herawaty Sebajang, Frank Schwenter, Ramses Wassef, Richard Ratelle, Éric De Broux, Carole Richard, Manuela M Santos","doi":"10.1186/s40168-025-02101-1","DOIUrl":"https://doi.org/10.1186/s40168-025-02101-1","url":null,"abstract":"<p><strong>Background: </strong>Colorectal cancer (CRC) development is influenced by both iron and gut microbiota composition. While iron supplementation is routinely used to manage anemia in CRC patients, it may also impact gut microbiota and promote tumorigenesis. In this study, we investigated the impact of initial gut microbiota composition on iron-promoted tumorigenesis. We performed fecal microbiota transplantation (FMT) in Apc^Min/+ mice using samples from healthy controls, CRC patients, and mice, followed by exposure to iron sufficient or iron excess diets.</p><p><strong>Results: </strong>We found that iron supplementation promoted CRC and resulted in distinct gut microbiota changes in Apc^Min/+ mice receiving FMT from CRC patients (FMT-CRC), but not from healthy controls or mice. Oral treatment with identified bacterial strains, namely Faecalibaculum rodentium, Holdemanella biformis, Bifidobacterium pseudolongum, and Alistipes inops, protected FMT-CRC mice against iron-promoted tumorigenesis.</p><p><strong>Conclusions: </strong>Our findings suggest that microbiota-targeted interventions may mitigate tumorigenic effects of iron supplementation in anemic patients with CRC.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"100"},"PeriodicalIF":13.8,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12013013/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144007868","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Systems genetics uncovers associations among host amylase locus, gut microbiome, and metabolic traits in mice.","authors":"Qijun Zhang, Evan R Hutchison, Calvin Pan, Matthew F Warren, Mark P Keller, Alan D Attie, Aldons J Lusis, Federico E Rey","doi":"10.1186/s40168-025-02093-y","DOIUrl":"10.1186/s40168-025-02093-y","url":null,"abstract":"<p><strong>Background: </strong>Population studies have revealed associations between host genetic and gut microbiome in humans and mice. However, the molecular bases for how host genetic variation impacts the gut microbial community and bacterial metabolic niches remain largely unknown.</p><p><strong>Results: </strong>We leveraged 90 inbred hyperlipidemic mouse strains from the hybrid mouse diversity panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these, we detected a genetic locus surrounding multiple amylase genes that were associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar degrading capabilities. The genetic variants at the amylase gene locus were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes.</p><p><strong>Conclusions: </strong>This work reveals novel relationships among host genetic variation, gut microbial enterotypes, and host metabolic traits and supports the notion that variation of host amylase may represent a key determinant of gut microbiome in mice. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"101"},"PeriodicalIF":13.8,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12012960/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003756","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}