Microbiome最新文献

{"title":"Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets.","authors":"Shankumar Mooyottu, Muhammed Shafeekh Muyyarikkandy, Farnaz Yousefi, Ganwu Li, Orhan Sahin, Eric Burrough, Joy Scaria, Brett Sponseller, Alejandro Ramirez","doi":"10.1186/s40168-025-02042-9","DOIUrl":"10.1186/s40168-025-02042-9","url":null,"abstract":"<p><strong>Background: </strong>Weaning-associated enteric diseases are a major concern in the swine industry. This study investigates the effects of fecal microbiota transplantation (FMT) on the jejunum of weanling piglets, a segment of bowel less studied in terms of microbiomic changes despite its primary involvement in major post-weaning enteric diseases, including postweaning diarrhea (PWD). Thirty-two 3-week-old piglets were divided equally into two groups: Control and FMT. The FMT group received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning. Half of each group was inoculated with an enterotoxigenic E. coli (ETEC) isolate 10 days post-FMT. Piglets were euthanized in the third week (14th and 18th days post-FMT) after weaning to collect intestinal tissues and contents for microbiomic, metabolomic, and transcriptomic analyses.</p><p><strong>Results: </strong>The jejunal microbiota showed a significant increase in alpha diversity in the third week post-FMT compared with the ileum and colon. FMT significantly enriched the jejunal microbiota composition, while multiple bacterial genera were specifically lacking in control weanling piglets. FMT was strongly associated with the enrichment of the genus Pseudoscardovia of the Bifidobacteriaceae family, which was found lacking in the jejunum of weanling control piglets and inversely associated with the abundance of the genus Bifidobacterium within the same family. Other genera associated with FMT included Solobacterium, Shuttleworthia, and Pseudoraminibacter, whereas bacteria such as Erysipelotrichaceae and Acidaminococcus were identified as most abundant in the control piglets. Metabolomic analysis revealed a significant modulatory effect of FMT on carbohydrate, amino acid, nucleotide, vitamin, and xenobiotic metabolisms, suggesting improved nutrient utilization. Transcriptomic analyses further confirmed the regulatory effects of FMT on gene expression associated with immune, metabolic, barrier, and neuroendocrine functions. Prior FMT treatment in the context of ETEC infection indicated a potential protective role, as evidenced by a significant shift in microbial diversity and metabolomic compositions and decreased diarrhea severity even though no effect on pathogen shedding was evident.</p><p><strong>Conclusions: </strong>This study underscores the promise of FMT in enhancing jejunal health. In addition, the results suggest that FMT could be considered a potential strategy to address conditions associated with small intestinal dysbiosis in swine and other monogastric species with similar gut anatomy and physiology, such as humans. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"45"},"PeriodicalIF":13.8,"publicationDate":"2025-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11803973/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143370870","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":"Metatranscriptomes-based sequence similarity networks uncover genetic signatures within parasitic freshwater microbial eukaryotes.","authors":"Arthur Monjot, Jérémy Rousseau, Lucie Bittner, Cécile Lepère","doi":"10.1186/s40168-024-02027-0","DOIUrl":"10.1186/s40168-024-02027-0","url":null,"abstract":"<p><strong>Background: </strong>Microbial eukaryotes play a crucial role in biochemical cycles and aquatic trophic food webs. Their taxonomic and functional diversity are increasingly well described due to recent advances in sequencing technologies. However, the vast amount of data produced by -omics approaches require data-driven methodologies to make predictions about these microorganisms' role within ecosystems. Using metatranscriptomics data, we employed a sequence similarity network-based approach to explore the metabolic specificities of microbial eukaryotes with different trophic modes in a freshwater ecosystem (Lake Pavin, France).</p><p><strong>Results: </strong>A total of 2,165,106 proteins were clustered in connected components enabling analysis of a great number of sequences without any references in public databases. This approach coupled with the use of an in-house trophic modes database improved the number of proteins considered by 42%. Our study confirmed the versatility of mixotrophic metabolisms with a large number of shared protein families among mixotrophic and phototrophic microorganisms as well as mixotrophic and heterotrophic microorganisms. Genetic similarities in proteins of saprotrophs and parasites also suggest that fungi-like organisms from Lake Pavin, such as Chytridiomycota and Oomycetes, exhibit a wide range of lifestyles, influenced by their degree of dependence on a host. This plasticity may occur at a fine taxonomic level (e.g., species level) and likely within a single organism in response to environmental parameters. While we observed a relative functional redundancy of primary metabolisms (e.g., amino acid and carbohydrate metabolism) nearly 130,000 protein families appeared to be trophic mode-specific. We found a particular specificity in obligate parasite-related Specific Protein Clusters, underscoring a high degree of specialization in these organisms.</p><p><strong>Conclusions: </strong>Although no universal marker for parasitism was identified, candidate genes can be proposed at a fine taxonomic scale. We notably provide several protein families that could serve as keys to understanding host-parasite interactions representing pathogenicity factors (e.g., involved in hijacking host resources, or associated with immune evasion mechanisms). All these protein families could offer valuable insights for developing antiparasitic treatments in health and economic contexts. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"43"},"PeriodicalIF":13.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143365027","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":"Soil warming increases the active antibiotic resistome in the gut of invasive giant African snails.","authors":"Yiyue Zhang, Hong-Zhe Li, Martin Breed, Zhonghui Tang, Li Cui, Yong-Guan Zhu, Xin Sun","doi":"10.1186/s40168-025-02044-7","DOIUrl":"10.1186/s40168-025-02044-7","url":null,"abstract":"<p><strong>Background: </strong>Global warming is redrawing the map for invasive species, spotlighting the globally harmful giant African snail as a major ecological disruptor and public health threat. Known for harboring extensive antibiotic resistance genes (ARGs) and human pathogens, it remains uncertain whether global warming exacerbates these associated health risks.</p><p><strong>Methods: </strong>We use phenotype-based single-cell Raman with D₂O labeling (Raman-D₂O) and genotype-based metagenomic sequencing to investigate whether soil warming increases active antibiotic-resistant bacteria (ARBs) in the gut microbiome of giant African snails.</p><p><strong>Results: </strong>We show a significant increase in beta-lactam phenotypic resistance of active ARBs with rising soil temperatures, mirrored by a surge in beta-lactamase genes such as SHV, TEM, OCH, OKP, and LEN subtypes. Through a correlation analysis between the abundance of phenotypically active ARBs and genotypically ARG-carrying gut microbes, we identify species that contribute to the increased activity of antibiotic resistome under soil warming. Among 299 high-quality ARG-carrying metagenome-assembled genomes (MAGs), we further revealed that the soil warming enhances the abundance of \"supercarriers\" including human pathogens with multiple ARGs and virulence factors. Furthermore, we identified elevated biosynthetic gene clusters (BGCs) within these ARG-carrying MAGs, with a third encoding at least one BGC. This suggests a link between active ARBs and secondary metabolism, enhancing the environmental adaptability and competitive advantage of these organisms in warmer environments.</p><p><strong>Conclusions: </strong>The study underscores the complex interactions between soil warming and antibiotic resistance in the gut microbiome of the giant African snail, highlighting a potential escalation in environmental health risks due to global warming. These findings emphasize the urgent need for integrated environmental and health strategies to manage the rising threat of antibiotic resistance in the context of global climate change. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"42"},"PeriodicalIF":13.8,"publicationDate":"2025-02-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11800439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143365053","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":"Extensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.","authors":"Carmen Molina-Pardines, Jose M Haro-Moreno, Francisco Rodriguez-Valera, Mario López-Pérez","doi":"10.1186/s40168-025-02037-6","DOIUrl":"10.1186/s40168-025-02037-6","url":null,"abstract":"<p><strong>Background: </strong>The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.</p><p><strong>Results: </strong>The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~ 81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).</p><p><strong>Conclusions: </strong>This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn, mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"41"},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796062/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189501","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":"Enhancing microbial predator-prey detection with network and trait-based analyses.","authors":"Cristina Martínez Rendón, Christina Braun, Maria Kappelsberger, Jens Boy, Angélica Casanova-Katny, Karin Glaser, Kenneth Dumack","doi":"10.1186/s40168-025-02035-8","DOIUrl":"10.1186/s40168-025-02035-8","url":null,"abstract":"<p><strong>Background: </strong>Network analyses are often applied to microbial communities using sequencing survey datasets. However, associations in such networks do not necessarily indicate actual biotic interactions, and even if they do, the nature of the interactions commonly remains unclear. While network analyses are valuable for generating hypotheses, the inferred hypotheses are rarely experimentally confirmed.</p><p><strong>Results: </strong>We employed cross-kingdom network analyses, applied trait-based functions to the microorganisms, and subsequently experimentally investigated the found putative predator-prey interactions to evaluate whether, and to what extent, correlations indicate actual predator-prey relationships. For this, we investigated algae and their protistan predators in biocrusts of three distinct polar regions, i.e., Svalbard, the Antarctic Peninsula, and Continental Antarctica. Network analyses using FlashWeave indicated that 89, 138, and 51 correlations occurred between predatory protists and algae, respectively. However, trait assignment revealed that only 4.7-9.3% of said correlations link predators to actually suitable prey. We further confirmed these results with HMSC modeling, which resulted in similar numbers of 7.5% and 4.8% linking predators to suitable prey for full co-occurrence and abundance models, respectively. The combination of network analyses and trait assignment increased confidence in the prediction of predator-prey interactions, as we show that 82% of all experimentally investigated correlations could be verified. Furthermore, we found that more vicious predators, i.e., predators with the highest growth rate in co-culture with their prey, exhibit higher stress and betweenness centrality - giving rise to the future possibility of determining important predators from their network statistics.</p><p><strong>Conclusions: </strong>Our results support the idea of using network analyses for inferring predator-prey interactions, but at the same time call for cautionary consideration of the results, by combining them with trait-based approaches to increase confidence in the prediction of biological interactions. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"37"},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792678/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189558","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":"Microbiota governs host chenodeoxycholic acid glucuronidation to ameliorate bile acid disorder induced diarrhea.","authors":"Zishen Lin, Yue Feng, Jinping Wang, Zhaoyue Men, Xi Ma","doi":"10.1186/s40168-024-02011-8","DOIUrl":"10.1186/s40168-024-02011-8","url":null,"abstract":"<p><strong>Background: </strong>Disorder in bile acid (BA) metabolism is known to be an important factor contributing to diarrhea. However, the pathogenesis of BA disorder-induced diarrhea remains unclear.</p><p><strong>Methods: </strong>The colonic BA pool and microbiota between health piglets and BA disorder-induced diarrheal piglets were compared. Fecal microbiota transplantation and various cell experiments further indicated that chenodeoxycholic acid (CDCA) metabolic disorder produced CDCA-3β-glucuronide, which is the main cause of BA disorder diarrhea. Non-targeted metabolomics uncovered the inhibition of the BA glucuronidation by Lactobacillus reuteri (L. reuteri) is through deriving indole-3-carbinol (I3C). In vitro, important gene involved in the reduction of BA disorder induced-diarrhea were screened by RNA transcriptomics sequencing, and activation pathway of FXR-SIRT1-LKB1 to alleviate BA disorder diarrhea and P53-mediated apoptosis were proposed in vitro by multifarious siRNA interference, CO-IP, immunofluorescence, and so on, which mechanism was also verified in a variety of mouse models.</p><p><strong>Results: </strong>Here, we reveal for the first time that core microbiota derived I3C represses gut epithelium glucuronidation, particularly 3β-glucuronic CDCA production, which reaction is mediated by host UDP glucuronosyltransferase family 1 member A4 (UGT1A4) and necessary of BA disorder induced diarrhea. Mechanistically, L. reuteri derived I3C activates aryl hydrocarbon receptor to decrease UGT1A4 transcription and CDCA-3β-glucuronide content, thereby upregulating FXR-SIRT1-LKB1 signal. LKB1 binds with P53 based on protein interaction, ultimately resists to apoptosis and diarrhea. Moreover, I3C assists CDCA to attain the ameliorative effects of FXR activation in BA disorder diarrhea, through reversion of abnormal metabolism pathway, improving the outcomes of CDCA supplement.</p><p><strong>Conclusion: </strong>These findings uncover the crucial interplay between gut epithelial cells and microbes, highlighting UGT1A4-mediated conversion of CDCA-3β-glucuronide as a key target for ameliorating BA disorder-induced diarrhea. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"36"},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792533/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189654","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 profiling of the vaginal microbiota improves resolution of the microbiota-immune axis.","authors":"Eric Armstrong, Rachel Liu, James Pollock, Sanja Huibner, Suji Udayakumar, Erastus Irungu, Pauline Ngurukiri, Peter Muthoga, Wendy Adhiambo, Sergey Yegorov, Joshua Kimani, Tara Beattie, Bryan Coburn, Rupert Kaul","doi":"10.1186/s40168-025-02039-4","DOIUrl":"10.1186/s40168-025-02039-4","url":null,"abstract":"<p><strong>Background: </strong>The composition of the vaginal microbiota is closely linked to adverse sexual and reproductive health outcomes, due in part to effects on genital immunology. Compositional approaches such as metagenomic sequencing provide a snapshot of all bacteria in a sample and have become the standard for characterizing the vaginal microbiota, but only provide microbial relative abundances. We hypothesized that the addition of absolute abundance data would provide a more complete picture of host-microbe interactions in the female genital tract.</p><p><strong>Results: </strong>We analyzed cervicovaginal secretions from 196 female sex workers in Kenya and found that bacterial load was elevated among women with diverse, bacterial vaginosis (BV)-type microbiota and lower among women with Lactobacillus predominance. Bacterial load was also positively associated with proinflammatory cytokines, such as IL-1α, and negatively associated with chemokines, such as IP-10. The associations between bacterial load and immune factors differed across bacterial community states, but L. crispatus predominance was the only microbial community where higher bacterial load was not associated with higher proinflammatory cytokines. Total vaginal bacterial load was also a stronger predictor of the genital immune environment than BV by Nugent score, the current clinical standard, in the Kenya-based cohort and in a Uganda-based confirmatory cohort.</p><p><strong>Conclusions: </strong>Our results suggest that total vaginal bacterial load is at least as strong a predictor of the genital immune milieu as current BV clinical diagnostic tools, supporting exploration of the vaginal bacterial load as a predictor of adverse reproductive and sexual health outcomes. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"39"},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792376/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189664","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":"De-biasing microbiome sequencing data: bacterial morphology-based correction of extraction bias and correlates of chimera formation.","authors":"Luise Rauer, Amedeo De Tomassi, Christian L Müller, Claudia Hülpüsch, Claudia Traidl-Hoffmann, Matthias Reiger, Avidan U Neumann","doi":"10.1186/s40168-024-01998-4","DOIUrl":"10.1186/s40168-024-01998-4","url":null,"abstract":"<p><strong>Introduction: </strong>Microbiome amplicon sequencing data are distorted by multiple protocol-dependent biases from bacterial DNA extraction, contamination, sequence errors, and chimeras, hindering clinical microbiome applications. In particular, extraction bias is a major confounder in sequencing-based microbiome analyses, with no correction method available to date. Here, we suggest using mock community controls to computationally correct extraction bias based on bacterial morphological properties.</p><p><strong>Methods: </strong>We compared dilution series of 3 cell mock communities with an even or staggered composition. DNA of these mock, and additional skin microbiome samples, was extracted with 8 different extraction protocols (2 buffers, 2 extraction kits, 2 lysis conditions). Extracted DNA was sequenced (V1-V3 16S rRNA gene) together with corresponding DNA mocks.</p><p><strong>Results: </strong>Microbiome composition was significantly different between extraction kits and lysis conditions, but not between buffers. Independent of the extraction protocol, chimera formation increased with higher input cell numbers. Contaminants originated mostly from buffers, and considerable cross-contamination was observed in low-input samples. Comparing the microbiome composition of the cell mocks to corresponding DNA mocks revealed taxon-specific protocol-dependent extraction bias. Strikingly, this extraction bias per species was predictable by bacterial cell morphology. Morphology-based computational correction of extraction bias significantly improved resulting microbial compositions when applied to different mock samples, even with different taxa. Equivalent correction of the skin samples showed a substantial impact on microbiome compositions.</p><p><strong>Conclusions: </strong>Our results indicate that higher DNA density increases chimera formation during PCR amplification. Furthermore, we show that computational correction of extraction bias based on bacterial cell morphology would be feasible using appropriate positive controls, thus constituting an important step toward overcoming protocol biases in microbiome analysis. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"38"},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11792448/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189484","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":"Global biogeography and projection of antimicrobial toxin genes.","authors":"Ya Liu, Yu Geng, Yiru Jiang, Jingyu Sun, Peng Li, Yue-Zhong Li, Zheng Zhang","doi":"10.1186/s40168-025-02038-5","DOIUrl":"10.1186/s40168-025-02038-5","url":null,"abstract":"<p><strong>Background: </strong>Antimicrobial toxin genes (ATGs) encode potent antimicrobial weapons in nature that rival antibiotics, significantly impacting microbial survival and offering potential benefits for human health. However, the drivers of their global diversity and biogeography remain unknown.</p><p><strong>Results: </strong>Here, we identified 4400 ATG clusters from 149 families by correlating 10,000 samples worldwide with over 200,000 microbial genome data. We demonstrated that global microbial communities universally encode complex and diverse ATGs, with widespread differences across various habitats. Most ATG clusters were rare within habitats but were shared among habitats. Compared with those in animal-associated habitats, ATG clusters in human-associated habitats exhibit greater diversity and a greater proportion of sharing with natural habitats. We generated a global atlas of ATG distribution, identifying anthropogenic factors as crucial in explaining ATG diversity hotspots.</p><p><strong>Conclusions: </strong>Our study provides baseline information on the global distribution of antimicrobial toxins by combining community samples, genome sequences, and environmental constraints. Our results highlight the natural environment as a reservoir of antimicrobial toxins, advance the understanding of the global distribution of these antimicrobial weapons, and aid their application in clinical, agricultural, and industrial fields. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"40"},"PeriodicalIF":13.8,"publicationDate":"2025-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11796102/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143189505","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":"Host selection is not a universal driver of phyllosphere community assembly among ecologically similar native New Zealand plant species.","authors":"Anya S Noble, Jaber Abbaszadeh, Charles K Lee","doi":"10.1186/s40168-024-02000-x","DOIUrl":"10.1186/s40168-024-02000-x","url":null,"abstract":"<p><strong>Background: </strong>A growing body of evidence demonstrates that host-associated microbial communities of plant leaf surfaces (i.e. the phyllosphere) can influence host functional traits. However, it remains unclear whether host selection is a universal driver of phyllosphere community assembly. We targeted mānuka (Leptospermum scoparium) and three neighbouring non-mānuka plant species along an 1800-m transect in a New Zealand native bush to conduct a hypothesis-driven investigation of the relative influence of host species identity and stochastic dispersal on the composition of natural phyllosphere bacterial communities.</p><p><strong>Results: </strong>We detected significant correlations between host species identity and mānuka phyllosphere communities that are consistent with a dominant role of host selection in the assembly of the mānuka phyllosphere microbiome. In contrast, the phyllosphere community compositions of neighbouring, ecologically similar native plants were highly variable, suggesting that stochastic processes, such as dispersal, had a stronger influence on the phyllosphere microbiomes of those non-mānuka plants compared to the phyllosphere microbiome of mānuka. Furthermore, the distribution of phyllosphere taxa among plant species was congruent with a scenario in which microorganisms had dispersed from mānuka to non-mānuka phyllosphere microbiomes.</p><p><strong>Conclusions: </strong>We conclude that host selection of phyllosphere communities is not and should not be presumed to be a universal trait across plant species. The specificity of the mānuka phyllosphere microbiome suggests the presence of functionally significant bacteria that are under direct, possibly chemically mediated, selection by the host. Furthermore, we propose that phyllosphere microbiomes under strong host selection, such as that of mānuka, may act as a source of microorganisms for the phyllosphere microbiomes of neighbouring plants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"13 1","pages":"35"},"PeriodicalIF":13.8,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11786578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143074927","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}