Microbiome最新文献

{"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":"<p><strong>Background: </strong>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.</p><p><strong>Results: </strong>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":"https://doi.org/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}

{"title":"Environmental yeasts differentially impact the development and oviposition behavior of the Asian tiger mosquito Aedes albopictus.","authors":"Simon Malassigné, Mathieu Laÿs, Laurent Vallon, Edwige Martin, Guillaume Meiffren, Aurélien Vigneron, Vân Tran Van, Guillaume Minard, Claire Valiente Moro, Patricia Luis","doi":"10.1186/s40168-025-02099-6","DOIUrl":"https://doi.org/10.1186/s40168-025-02099-6","url":null,"abstract":"<p><strong>Background: </strong>While the Asian tiger mosquito (Aedes albopictus), a known vector of many arboviruses, establishes symbiotic associations with environmentally acquired yeasts, their impact on mosquito biology remains poorly investigated. To better understand these associations, we hypothesized that waterborne yeasts colonizing the larval gut differentially support mosquito development based on their capacity to produce riboflavin or recycle nitrogen waste into proteins by secreting uricase, as B vitamins and amino acids are crucial for mosquito development. To address this hypothesis, we used axenic and gnotobiotic insects to gauge the specific impact of different environmental yeasts on Ae. albopictus development and survival. We then evaluated whether the observed variations across yeast species could be linked to differential uricolytic activities and varying quantities of riboflavin and proteins in insecta. Finally, given that mosquito oviposition site selection favors conditions that enhance offspring performance, we tested whether yeasts that promote faster development mediate oviposition site selection by gravid females.</p><p><strong>Results: </strong>Differences in mosquito development times were observed based on the environmental yeast used. Yeasts like Rhodotorula mucilaginosa and Aureobasidium pullulans promoted rapid development and were associated with improved survival. Conversely, yeasts such as Torulaspora delbrueckii and Martiniozyma asiatica, which led to slower development, produced smaller adults. Notably, R. mucilaginosa, which promoted the fastest development, provided high riboflavin intakes and enhance nitrogenous waste recycling and protein synthesis through strong uricolytic-ureolytic activity. Behavioral experiments indicated that yeasts promoting rapid development \"attract gravid females.</p><p><strong>Conclusions: </strong>Our findings highlight that a set of environmental yeasts present in natural larval breeding sites can be associated with improved mosquito development and survival by enhancing nutritional intake, thereby attracting gravid females. Variations in mosquito development time are likely linked to the differential levels of riboflavin production and nitrogenous waste recycling capacities among yeast species. This study opens new perspectives on the trophic interactions between mosquitoes and their mycobiota, emphasizing the importance of nitrogen-containing molecules such as essential amino acids, proteins, or vitamins provided by the mycobiota. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"99"},"PeriodicalIF":13.8,"publicationDate":"2025-04-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12004758/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144018103","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":"Effect of inulin supplementation in maternal fecal microbiota transplantation on the early growth of chicks.","authors":"Mengxian Chen, Junxing Pan, Yang Song, Shenao Liu, Peng Sun, Xin Zheng","doi":"10.1186/s40168-025-02084-z","DOIUrl":"10.1186/s40168-025-02084-z","url":null,"abstract":"<p><strong>Background: </strong>Fecal microbial transplantation (FMT) is an important technology for treating diarrhea and enteritis. Additionally, FMT has been applied to improve productivity, alter abnormal behavior, relieve stress, and reduce burdens. However, some previous studies have reported that FMT may cause stress in acceptor animals. Inulin, a prebiotic, can promote growth, enhance immunity, and balance the gut microbiota. Currently, there are limited reports on the effects of combining FMT with inulin on early growth performance in chicks.</p><p><strong>Results: </strong>In this study, a total of 90 1-day-old chicks were randomly divided into the control group (CON), FMT group, and inulin group (INU). The CON group was fed a basic diet, whereas the FMT and INU groups received fecal microbiota transplantation and FMT with inulin treatment, respectively. Compared with the FMT and CON groups, the INU group presented significantly greater average daily gain (ADG) and average daily feed intake (ADFI) values (P < 0.05). However, the organ indices did not significantly change (P > 0.05). The ratio of the villi to crypts in the ileum significantly differed at 21 and 35 days (P < 0.05). In addition, the cecum concentrations of acetic acid and butyric acid significantly increased in the INU group (P < 0.05). In addition, gut inflammation and serum inflammation decreased in the INU group, and immune factors increased after inulin supplementation. (P < 0.05). Firmicutes and Bacteroidetes were the dominant phyla, with more than 90% of all sequences being identified as originating from these two phyla. Inulin supplementation during mother-sourced microbial transplantation significantly increased the abundance of Rikenella, Butyricicoccus, and [Ruminococcus], which contributed positively to the promotion of early intestinal health and facilitated the early growth of chicks.</p><p><strong>Conclusion: </strong>The results of this study suggest that inulin supplementation in maternal fecal microbiota transplantation can effectively promote early growth and probiotic colonization, which favors the health of chicks. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"98"},"PeriodicalIF":13.8,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11998286/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144001472","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":"Cognitive and behavioral benefits of 2'-fucosyllactose in growing mice: the roles of 5-hydroxytryptophan and gut microbiota.","authors":"Liuying Zhu, Zhiyi Zhang, Ting Luo, Hongyan Li, Zeyuan Deng, Jing Li, Liufeng Zheng, Jinqiang Liao, Minghui Wang, Bing Zhang","doi":"10.1186/s40168-025-02094-x","DOIUrl":"https://doi.org/10.1186/s40168-025-02094-x","url":null,"abstract":"<p><strong>Background: </strong>2'-Fucosyllactose (2'-FL) is one of the major oligosaccharides found in human breast milk, with several recognized beneficial effects on the host. Extensive research has indicated positive effects of 2'-FL on cognitive development in the brain, yet its molecular mechanisms have remained elusive. This study aimed to assess the impact of 2'-FL on the gut-brain axis microbiota and cognitive function in growing mice, along with its potential mechanisms of action.</p><p><strong>Results: </strong>Following long-term supplementation for 4 weeks, 2'-FL was found to enhance cognitive memory function in growing mice (3 weeks old) as assessed through Y-maze, novel object recognition, and water maze tests. Analysis via 16S rRNA sequencing revealed significant alterations in gut microbiota diversity and composition induced by 2'-FL, notably increasing the relative abundance of Bacteroides and Lactobacillus genera. Additionally, 2'-FL significantly elevated levels of 5-hydroxytryptamine (5-HT) and 5-hydroxytryptophan (5-HTP) in the hippocampal tissue. However, antibiotic intervention abolished the cognitive advantage conferred by 2'-FL, highlighting the critical role of gut microbiota in mediating its effects. Similarly, short-term supplementation with 2'-FL for 7 days indicated rapid changes in gut microbiota composition preceding cognitive improvements, further suggesting a potential causal relationship between gut microbiota characteristics and cognition. Further, in vitro experiments with mouse feces suggested that 2'-FL may influence tryptophan hydroxylase levels in the gut microbiota and inhibit the activity of 5-hydroxytryptophan decarboxylase, potentially leading to increased accumulation of 5-HTP. Additionally, 2'-FL may indirectly impact tryptophan hydroxylase levels in enterochromaffin cells by promoting short-chain fatty acid production, which could support 5-HTP synthesis. Elevated 5-HTP produced by the gut system enters the bloodstream, crosses the blood-brain barrier, and may potentially enhance brain 5-HT levels.</p><p><strong>Conclusion: </strong>This study offers preliminary evidence that the cognitive-promoting effects of 2'-FL in mice may be closely associated with gut microbiota and 5-HT. The findings suggest that 2'-FL contribute to cognitive development in growing mice, potentially by modulating gut microbiota and enhancing 5-HT levels in the brain. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"97"},"PeriodicalIF":13.8,"publicationDate":"2025-04-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11992797/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143989787","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":"House dust microbiome differentiation and phage-mediated antibiotic resistance and virulence dissemination in the presence of endocrine-disrupting chemicals and pharmaceuticals.","authors":"Shicong Du, Huiju Lin, Qiong Luo, Chung Ling Man, Sze Han Lai, Kin Fai Ho, Kenneth M Y Leung, Patrick K H Lee","doi":"10.1186/s40168-025-02081-2","DOIUrl":"https://doi.org/10.1186/s40168-025-02081-2","url":null,"abstract":"<p><strong>Background: </strong>House dust serves as a reservoir of a diverse array of microbial life and anthropogenic chemicals, both of which can potentially influence the health of occupants, particularly those who spend significant amounts of time at home. However, the effects of anthropogenic chemicals on dust microbiomes remain poorly understood. This study investigated the presence of anthropogenic chemicals in the dust of homes occupied by elderly occupants and explored those chemicals' relationships with dust microbiomes.</p><p><strong>Results: </strong>We detected 69 out of 76 analyzed anthropogenic chemicals, including endocrine-disrupting chemicals, non-antibiotic pharmaceuticals, and antibiotics, in at least one house dust sample from 32 residential homes, with concentrations ranging from 2720 to 89,300 ng/g. Some of these detected compounds were pharmaceuticals regularly consumed by the occupants. The dust microbiomes were associated with varying levels of anthropogenic chemicals, forming two distinct clusters, each with unique diversity, taxonomy, metabolic functions, and resistome profiles. Higher concentrations and a greater variety of these chemicals were associated with an increased co-occurrence of antibiotic resistance and virulence genes, as well as an enhanced potential for their transfer through mobile genetic elements. Under these conditions, phages, especially phage-plasmids, facilitated the dissemination of antibiotic resistance and virulence among bacterial populations.</p><p><strong>Conclusions: </strong>The findings indicate that everyday anthropogenic chemicals are important factors associated with the microbes in indoor environments. This underscores the importance of improving household chemical stewardship to reduce the health risks associated with exposure to these chemicals and their effects on indoor microbiomes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"96"},"PeriodicalIF":13.8,"publicationDate":"2025-04-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11980161/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144028703","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":"A blueprint for contemporary studies of microbiomes.","authors":"Laure B Bindels, Joy E M Watts, Kevin R Theis, Víctor J Carrion, Adam Ossowicki, Jana Seifert, Julia Oh, Yongqi Shao, Markus Hilty, Purnima Kumar, Falk Hildebrand, Connie Lovejoy, Paul Wigley, Ke Yu, Meiling Zhang, Tong Zhang, Jens Walter, Mahesh S Desai, Sharon Ann Huws, Lynn M Schriml, Jacques Ravel, W Florian Fricke, Emiley A Eloe-Fadrosh, Charles K Lee, Thomas Clavel","doi":"10.1186/s40168-025-02091-0","DOIUrl":"10.1186/s40168-025-02091-0","url":null,"abstract":"<p><p>This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opportunity to clarify our expectations for the articles submitted to the journal. At Microbiome, we are seeking studies that provide either new mechanistic insights into the role of microbiomes in health and environmental systems or substantial conceptual or technical advances. Manuscripts need to meet high standards of language accuracy, quality of microbiome analyses, and data and protocol availability, including detailed reporting of wet-lab and in silico protocols, all of which can critically enhance transparency and reproducibility. We think that such efforts are essential to push the boundaries of our knowledge on microbiomes in a concerted, international effort.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"95"},"PeriodicalIF":13.8,"publicationDate":"2025-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11977902/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143811690","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":"Candidate Phyla Radiation (CPR) bacteria from hyperalkaline ecosystems provide novel insight into their symbiotic lifestyle and ecological implications.","authors":"Yu He, Shiyan Zhuo, Meng Li, Jie Pan, Yongguang Jiang, Yidan Hu, Robert A Sanford, Qin Lin, Weimin Sun, Na Wei, Shuming Peng, Zhou Jiang, Shuyi Li, Yongzhe Li, Yiran Dong, Liang Shi","doi":"10.1186/s40168-025-02077-y","DOIUrl":"10.1186/s40168-025-02077-y","url":null,"abstract":"<p><strong>Background: </strong>Candidate Phyla Radiation (CPR) represents a unique superphylum characterized by ultra-small cell size and symbiotic lifestyle. Although CPR bacteria have been identified in varied environments, their broader distribution, associations with hosts, and ecological roles remain largely unexplored. To address these knowledge gaps, a serpentinite-like environment was selected as a simplified model system to investigate the CPR communities in hyperalkaline environments and their association with hosts in extreme conditions. Additionally, the enzymatic activity, global distribution, and evolution of the CPR-derived genes encoding essential metabolites (e.g., folate or vitamin B₉) were analyzed and assessed.</p><p><strong>Results: </strong>In the highly alkaline serpentinite-like ecosystem (pH = 10.9-12.4), metagenomic analyses of the water and sediment samples revealed that CPR bacteria constituted 1.93-34.8% of the microbial communities. Metabolic reconstruction of 12 high-quality CPR metagenome-assembled genomes (MAGs) affiliated to the novel taxa from orders UBA6257, UBA9973, and Paceibacterales suggests that these bacteria lack the complete biosynthetic pathways for amino acids, lipids, and nucleotides. Notably, the CPR bacteria commonly harbored the genes associated with essential folate cofactor biosynthesis and metabolism, including dihydrofolate reductase (folA), serine hydroxymethyltransferase (glyA), and methylenetetrahydrofolate reductase (folD). Additionally, two presumed auxotrophic hosts, incapable of forming tetrahydrofolate (THF) due to the absence of folA, were identified as potential hosts for some CPR bacteria harboring folA genes. The functionality of these CPR-derived folA genes was experimentally verified by heterologous expression in the folA-deletion mutant Escherichia coli MG1655 ΔfolA. Further assessment of the available CPR genomes (n = 4,581) revealed that the genes encoding the proteins for the synthesis of bioactive folate derivatives (e.g., folA, glyA, and/or folD genes) were present in 90.8% of the genomes examined. It suggests potential widespread metabolic complementarity in folate biosynthesis between CPR and their hosts.</p><p><strong>Conclusions: </strong>This finding deepens our understanding of the mechanisms of CPR-host symbiosis, providing novel insight into essential cofactor-dependent mutualistic CPR-host interactions. Our observations suggest that CPR bacteria may contribute to auxotrophic organisms and indirectly influence biogeochemical processes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"94"},"PeriodicalIF":13.8,"publicationDate":"2025-04-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11974145/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143795770","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}