Microbiome最新文献

{"title":"Distinct microbes, metabolites, and the host genome define the multi-omics profiles in right-sided and left-sided colon cancer.","authors":"Lei Liang, Cheng Kong, Jinming Li, Guang Liu, Jinwang Wei, Guan Wang, Qinying Wang, Yongzhi Yang, Debing Shi, Xinxiang Li, Yanlei Ma","doi":"10.1186/s40168-024-01987-7","DOIUrl":"10.1186/s40168-024-01987-7","url":null,"abstract":"<p><strong>Background: </strong>Studies have reported clinical heterogeneity between right-sided colon cancer (RCC) and left-sided colon cancer (LCC). However, none of these studies used multi-omics analysis combining genetic regulation, microbiota, and metabolites to explain the site-specific difference.</p><p><strong>Methods: </strong>Here, 494 participants from a 16S rRNA gene sequencing cohort (50 RCC, 114 LCC, and 100 healthy controls) and a multi-omics cohort (63 RCC, 79 LCC, and 88 healthy controls) were analyzed. 16S rRNA gene, metagenomic sequencing, and metabolomics analyses of fecal samples were evaluated to identify tumor location-related bacteria and metabolites. Whole-exome sequencing (WES) and transcriptome sequencing (RNA-seq) were conducted to obtain the mutation burden and genomic expression pattern.</p><p><strong>Results: </strong>We found unique profiles of the intestinal microbiome, metabolome, and host genome between RCC and LCC. The bacteria Flavonifractor plautii (Fp) and Fusobacterium nucleatum, the metabolites L-phenylalanine, and the host genes PHLDA1 and WBP1 were the key omics features of RCC; whereas the bacteria Bacteroides sp. A1C1 (B.A1C1) and Parvimonas micra, the metabolites L-citrulline and D-ornithine, and the host genes TCF25 and HLA-DRB5 were considered the dominant omics features in LCC. Multi-omics correlation analysis indicated that RCC-enriched Fp was related to the accumulation of the metabolite L-phenylalanine and the suppressed WBP1 signal in RCC patients. In addition, LCC-enriched B.A1C1 was associated with the accumulation of the metabolites D-ornithine and L-citrulline as well as activation of the genes TCF25, HLA-DRB5, and AC079354.1.</p><p><strong>Conclusion: </strong>Our findings identify previously unknown links between intestinal microbiota alterations, metabolites, and host genomics in RCC vs. LCC, suggesting that it may be possible to treat colorectal cancer (CRC) by targeting the gut microbiota-host interaction. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"274"},"PeriodicalIF":13.8,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11681701/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895781","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":"Metagenome-validated combined amplicon sequencing and text mining-based annotations for simultaneous profiling of bacteria and fungi: vaginal microbiota and mycobiota in healthy women.","authors":"Seppo Virtanen, Schahzad Saqib, Tinja Kanerva, Rebecka Ventin-Holmberg, Pekka Nieminen, Tiina Holster, Ilkka Kalliala, Anne Salonen","doi":"10.1186/s40168-024-01993-9","DOIUrl":"10.1186/s40168-024-01993-9","url":null,"abstract":"<p><strong>Background: </strong>Amplicon sequencing of kingdom-specific tags such as 16S rRNA gene for bacteria and internal transcribed spacer (ITS) region for fungi are widely used for investigating microbial communities. So far most human studies have focused on bacteria while studies on host-associated fungi in health and disease have only recently started to accumulate. To enable cost-effective parallel analysis of bacterial and fungal communities in human and environmental samples, we developed a method where 16S rRNA gene and ITS1 amplicons were pooled together for a single Illumina MiSeq or HiSeq run and analysed after primer-based segregation. Taxonomic assignments were performed with Blast in combination with an iterative text-extraction-based filtration approach, which uses extensive literature records from public databases to select the most probable hits that were further validated by shotgun metagenomic sequencing.</p><p><strong>Results: </strong>Using 50 vaginal samples, we show that the combined run provides comparable results on bacterial composition and diversity to conventional 16S rRNA gene amplicon sequencing. The text-extraction-based taxonomic assignment-guided tool provided ecosystem-specific bacterial annotations that were confirmed by shotgun metagenomic sequencing (VIRGO, MetaPhlAn, Kraken2). Fungi were identified in 39/50 samples with ITS sequencing while in the metagenome data fungi largely remained undetected due to their low abundance and database issues. Co-abundance analysis of bacteria and fungi did not show strong between-kingdom correlations within the vaginal ecosystem of healthy women.</p><p><strong>Conclusion: </strong>Combined amplicon sequencing for bacteria and fungi provides a simple and cost-effective method for simultaneous analysis of microbiota and mycobiota within the same samples. Conventional metagenomic sequencing does not provide sufficient fungal genome coverage for their reliable detection in vaginal samples. Text extraction-based annotation tool facilitates ecosystem-specific characterization and interpretation of microbial communities by coupling sequence homology to microbe metadata readily available through public databases. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"273"},"PeriodicalIF":13.8,"publicationDate":"2024-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11681650/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142895801","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":"Screening and identification of antimicrobial peptides from the gut microbiome of cockroach Blattella germanica.","authors":"Sizhe Chen, Huitang Qi, Xingzhuo Zhu, Tianxiang Liu, Yuting Fan, Qi Su, Qiuyu Gong, Cangzhi Jia, Tian Liu","doi":"10.1186/s40168-024-01985-9","DOIUrl":"10.1186/s40168-024-01985-9","url":null,"abstract":"<p><strong>Background: </strong>The overuse of antibiotics has led to lethal multi-antibiotic-resistant microorganisms around the globe, with restricted availability of novel antibiotics. Compared to conventional antibiotics, evolutionarily originated antimicrobial peptides (AMPs) are promising alternatives to address these issues. The gut microbiome of Blattella germanica represents a previously untapped resource of naturally evolving AMPs for developing antimicrobial agents.</p><p><strong>Results: </strong>Using the in-house designed tool \"AMPidentifier,\" AMP candidates were mined from the gut microbiome of B. germanica, and their activities were validated both in vitro and in vivo. Among filtered candidates, AMP1, derived from the symbiotic microorganism Blattabacterium cuenoti, demonstrated broad-spectrum antibacterial activity, low cytotoxicity towards mammalian cells, and a lack of hemolytic effects. Mechanistic studies revealed that AMP1 rapidly permeates the bacterial cell and accumulates intracellularly, resulting in a gradual and mild depolarization of the cell membrane during the initial incubation period, suggesting minimal direct impact on membrane integrity. Furthermore, observations from fluorescence microscopy and scanning electron microscopy indicated abnormalities in bacterial binary fission and compromised cell structure. These findings led to the hypothesis that AMP1 may inhibit bacterial cell wall synthesis. Furthermore, AMP1 showed potent antibacterial and wound healing effects in mice, with comparable performances of vancomycin.</p><p><strong>Conclusions: </strong>This study exemplifies an interdisciplinary approach to screening safe and effective AMPs from natural biological tissues, and our identified AMP 1 holds promising potential for clinical application.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"272"},"PeriodicalIF":13.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11663339/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872542","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":"Vaginal metatranscriptome meta-analysis reveals functional BV subgroups and novel colonisation strategies.","authors":"Scott J Dos Santos, Clara Copeland, Jean M Macklaim, Gregor Reid, Gregory B Gloor","doi":"10.1186/s40168-024-01992-w","DOIUrl":"10.1186/s40168-024-01992-w","url":null,"abstract":"<p><strong>Background: </strong>The application of '-omics' technologies to study bacterial vaginosis (BV) has uncovered vast differences in composition and scale between the vaginal microbiomes of healthy and BV patients. Compared to amplicon sequencing and shotgun metagenomic approaches focusing on a single or few species, investigating the transcriptome of the vaginal microbiome at a system-wide level can provide insight into the functions which are actively expressed and differential between states of health and disease.</p><p><strong>Results: </strong>We conducted a meta-analysis of vaginal metatranscriptomes from three studies, split into exploratory (n = 42) and validation (n = 297) datasets, accounting for the compositional nature of sequencing data and differences in scale between healthy and BV microbiomes. Conducting differential expression analyses on the exploratory dataset, we identified a multitude of strategies employed by microbes associated with states of health and BV to evade host cationic antimicrobial peptides (CAMPs); putative mechanisms used by BV-associated species to resist and counteract the low vaginal pH; and potential approaches to disrupt vaginal epithelial integrity so as to establish sites for adherence and biofilm formation. Moreover, we identified several distinct functional subgroups within the BV population, distinguished by genes involved in motility, chemotaxis, biofilm formation and co-factor biosynthesis. After defining molecular states of health and BV in the validation dataset using KEGG orthology terms rather than community state types, differential expression analysis confirmed earlier observations regarding CAMP resistance and compromising epithelial barrier integrity in healthy and BV microbiomes and also supported the existence of motile vs. non-motile subgroups in the BV population. These findings were independent of the enzyme classification system used (KEGG or EggNOG).</p><p><strong>Conclusions: </strong>Our findings highlight a need to focus on functional rather than taxonomic differences when considering the role of microbiomes in disease and identify pathways for further research as potential BV treatment targets. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"271"},"PeriodicalIF":13.8,"publicationDate":"2024-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662499/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872544","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":"New insights into the combined effects of aflatoxin B1 and Eimeria ovinoidalis on uterine function by disrupting the gut-blood-reproductive axis in sheep.","authors":"Shu-Cheng Huang, Kai-Li Liu, Pan Chen, Bo-Wen Xu, Wen-Li Ding, Tao-Jing Yue, Ya-Nan Lu, Sen-Yang Li, Jia-Kui Li, Fu-Chun Jian","doi":"10.1186/s40168-024-01966-y","DOIUrl":"10.1186/s40168-024-01966-y","url":null,"abstract":"<p><strong>Background: </strong>Sheep coccidiosis is an infectious parasitic disease that primarily causes diarrhea and growth retardation in young animals, significantly hindering the development of the sheep breeding industry. Cereal grains and animal feeds are frequently contaminated with mycotoxins worldwide, with aflatoxin B1 (AFB1) being the most common form. AFB1 poses a serious threat to gastrointestinal health upon ingestion and affects the function of parenteral organs, thus endangering livestock health. However, the impact of the combined effects of coccidia and AFB1 on the reproductive system of sheep has not been reported. Therefore, this study utilized sheep as an animal model to investigate the mechanisms underlying the reproductive toxicity induced by the individual or combined effects of AFB1 and Eimeria ovinoidalis (E. ovinoidalis) on the gut-blood-reproductive axis.</p><p><strong>Results: </strong>The results showed that AFB1 and coccidia adversely affect the reproductive system defense of sheep by altering uterine histopathology and hormone levels and triggering inflammation, which is associated with changes in the gut microbiota and metabolites. Moreover, co-exposure to AFB1 and coccidia disrupted the intestinal structure of the colon, resulting in reduced crypt depth. The impaired barrier function of the colon manifests primarily through the suppression of barrier protein expression, changes in the gut microbiome composition, and disruptions in gut metabolism. Importantly, the levels of blood inflammatory factors (IL-6, IL-10, TNF-α, and LPS) increased, suggesting that exposure to AFB1 and coccidia compromises the function of uterine organs in sheep by perturbing the gut-blood-reproductive axis. Blood metabolomics analysis further revealed that the differential metabolites predominantly concentrate in the amino acid pathway, particularly N-acetyl-L-phenylalanine. This metabolite is significantly correlated with IL-6, TNF-α, LPS, ERα, and ERβ, and it influences hormone levels while inducing uterine damage through the regulation of the downstream genes PI3K, AKT, and eNOS in the relaxin signaling pathway, as demonstrated by RNA sequencing.</p><p><strong>Conclusions: </strong>These findings reveal for the first time that the combined effects of AFB1 and E. ovinoidalis on sheep uterine function operate at the level of the gut-blood-reproductive axis. This suggests that regulating gut microbiota and its metabolites may represent a potential therapeutic strategy for addressing mycotoxins and coccidia-co-induced female reproductive toxicity.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"269"},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662449/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872540","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":"Complementary insights into gut viral genomes: a comparative benchmark of short- and long-read metagenomes using diverse assemblers and binners.","authors":"Huarui Wang, Chuqing Sun, Yun Li, Jingchao Chen, Xing-Ming Zhao, Wei-Hua Chen","doi":"10.1186/s40168-024-01981-z","DOIUrl":"10.1186/s40168-024-01981-z","url":null,"abstract":"<p><strong>Background: </strong>Metagenome-assembled viral genomes have significantly advanced the discovery and characterization of the human gut virome. However, we lack a comparative assessment of assembly tools on the efficacy of viral genome identification, particularly across next-generation sequencing (NGS) and third-generation sequencing (TGS) data.</p><p><strong>Results: </strong>We evaluated the efficiency of NGS, TGS, and hybrid assemblers for viral genome discovery using 95 viral-like particle (VLP)-enriched fecal samples sequenced on both Illumina and PacBio platforms. MEGAHIT, metaFlye, and hybridSPAdes emerged as the optimal choices for NGS, TGS, and hybrid datasets, respectively. Notably, these assemblers recovered distinct viral genomes, demonstrating a remarkable degree of complementarity. By combining individual assembler results, we expanded the total number of nonredundant high-quality viral genomes by 4.83 ~ 21.7-fold compared to individual assemblers. Among them, viral genomes from NGS and TGS data have the least overlap, indicating the impact of data type on viral genome recovery. We also evaluated four binning methods, finding that CONCOCT incorporated more unrelated contigs into the same bins, while MetaBAT2, AVAMB, and vRhyme balanced inclusiveness and taxonomic consistency within bins.</p><p><strong>Conclusions: </strong>Our findings highlight the challenges in metagenome-driven viral discovery, underscoring tool limitations. We advocate for combined use of multiple assemblers and sequencing technologies when feasible and highlight the urgent need for specialized tools tailored to gut virome assembly. This study contributes essential insights for advancing viral genome research in the context of gut metagenomics. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"260"},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11660840/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872458","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":"Shotgun metagenomic sequencing reveals the influence of artisanal dairy environments on the microbiomes, quality, and safety of Idiazabal, a raw ewe milk PDO cheese.","authors":"Gorka Santamarina-García, Min Yap, Fiona Crispie, Gustavo Amores, Cathy Lordan, Mailo Virto, Paul D Cotter","doi":"10.1186/s40168-024-01980-0","DOIUrl":"10.1186/s40168-024-01980-0","url":null,"abstract":"<p><strong>Background: </strong>Numerous studies have highlighted the impact of bacterial communities on the quality and safety of raw ewe milk-derived cheeses. Despite reported differences in the microbiota among cheese types and even producers, to the best of our knowledge, no study has comprehensively assessed all potential microbial sources and their contributions to any raw ewe milk-derived cheese, which could suppose great potential for benefits from research in this area. Here, using the Protected Designation of Origin Idiazabal cheese as an example, the impact of the environment and practices of artisanal dairies (including herd feed, teat skin, dairy surfaces, and ingredients) on the microbiomes of the associated raw milk, whey, and derived cheeses was examined through shotgun metagenomic sequencing.</p><p><strong>Results: </strong>The results revealed diverse microbial ecosystems across sample types, comprising more than 1300 bacterial genera and 3400 species. SourceTracker analysis revealed commercial feed and teat skin as major contributors to the raw milk microbiota (45.6% and 33.5%, respectively), being a source of, for example, Lactococcus and Pantoea, along with rennet contributing to the composition of whey and cheese (17.4% and 41.0%, respectively), including taxa such as Streptococcus, Pseudomonas_E or Lactobacillus_H. Functional analysis linked microbial niches to cheese quality- and safety-related metabolic pathways, with brine and food contact surfaces being most relevant, related to genera like Brevibacterium, Methylobacterium, or Halomonas. With respect to the virulome (virulence-associated gene profile), in addition to whey and cheese, commercial feed and grass were the main reservoirs (related to, e.g., Brevibacillus_B or CAG-196). Similarly, grass, teat skin, or rennet were the main contributors of antimicrobial resistance genes (e.g., Bact-11 or Bacteriodes_B). In terms of cheese aroma and texture, apart from the microbiome of the cheese itself, brine, grass, and food contact surfaces were key reservoirs for hydrolase-encoding genes, originating from, for example, Lactococcus, Lactobacillus, Listeria or Chromohalobacter. Furthermore, over 300 metagenomic assembled genomes (MAGs) were generated, including 60 high-quality MAGs, yielding 28 novel putative species from several genera, e.g., Citricoccus, Corynebacterium, or Dietzia.</p><p><strong>Conclusion: </strong>This study emphasizes the role of the artisanal dairy environments in determining cheese microbiota and, consequently, quality and safety. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"262"},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662609/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872543","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":"Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function.","authors":"Audrey Byrne, Christian Diener, Bryan P Brown, Brandon S Maust, Colin Feng, Berenice L Alinde, Sean M Gibbons, Meghan Koch, Clive M Gray, Heather B Jaspan, Donald D Nyangahu","doi":"10.1186/s40168-024-01973-z","DOIUrl":"10.1186/s40168-024-01973-z","url":null,"abstract":"<p><strong>Background: </strong>Infants exposed to HIV but uninfected have altered immune profiles which include heightened systemic inflammation. The mechanism(s) underlying this phenomenon is unknown. Here, we investigated differences in neonatal gut bacterial and viral microbiome and associations with inflammatory biomarkers in plasma. Further, we tested whether HIV exposure impacts antibody-microbiota binding in neonatal gut and whether antibodies in breast milk impact the growth of commensal bacteria.</p><p><strong>Results: </strong>Neonates exposed to HIV but uninfected (nHEU) exhibited altered gut bacteriome and virome compared to unexposed neonates (nHU). In addition, HIV exposure differentially impacted IgA-microbiota binding in neonates. The relative abundance of Blautia spp. in the whole stool or IgA-bound microbiota was positively associated with plasma concentrations of C-reactive protein. Finally, IgA from the breast milk of mothers living with HIV displayed a significantly lower ability to inhibit the growth of Blautia coccoides which was associated with inflammation in nHEU.</p><p><strong>Conclusion: </strong>nHEU exhibits profound alterations in gut bacterial microbiota with a mild impact on the enteric DNA virome. Elevated inflammation in nHEU could be due to a lower capacity of breast milk IgA from mothers living with HIV to limit growth the of gut bacteria associated with inflammation. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"261"},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662858/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872539","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 salt-tolerant growth-promoting phyllosphere microbial combination from mangrove plants and its mechanism for promoting salt tolerance in rice.","authors":"Xiangxia Yang, Rongwei Yuan, Shuangyu Yang, Zhian Dai, Na Di, Haijun Yang, Zhili He, Mi Wei","doi":"10.1186/s40168-024-01969-9","DOIUrl":"10.1186/s40168-024-01969-9","url":null,"abstract":"<p><strong>Background: </strong>Mangrove plants growing in the high salt environment of coastal intertidal zones colonize a variety of microorganisms in the phyllosphere, which have potential salt-tolerant and growth-promoting effects. However, the characteristics of microbial communities in the phyllosphere of mangrove species with and without salt glands and the differences between them remain unknown, and the exploration and the agricultural utilization of functional microbial resources from the leaves of mangrove plants are insufficient.</p><p><strong>Results: </strong>In this study, we examined six typical mangrove species to unravel the differences in the diversity and structure of phyllosphere microbial communities between mangrove species with or without salt glands. Our results showed that a combination of salt-tolerant growth-promoting strains of Pantoea stewartii A and Bacillus marisflavi Y25 (A + Y25) was constructed from the phyllosphere of mangrove plants, which demonstrated an ability to modulate osmotic substances in rice and regulate the expression of salt-resistance-associated genes. Further metagenomic analysis revealed that exogenous inoculation with A + Y25 increased the rice rhizosphere's specific microbial taxon Chloroflexi, thereby elevating microbial community quorum sensing and ultimately enhancing ionic balance and overall microbial community function to aid salt resistance in rice.</p><p><strong>Conclusions: </strong>This study advances our understanding of the mutualistic and symbiotic relationships between mangrove species and their phyllosphere microbial communities. It offers a paradigm for exploring agricultural beneficial microbial resources from mangrove leaves and providing the potential for applying the salt-tolerant bacterial consortium to enhance crop adaptability in saline-alkaline land. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"270"},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662529/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872532","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":"Asymmetric succession in soil microbial communities enhances the competitive advantage of invasive alien plants.","authors":"Mengxin Zhao, Yunfeng Yang, Han Zhang, Qiao Li, Xiaoxun Zhao, Xue Guo, Wanxue Liu, Fanghao Wan","doi":"10.1186/s40168-024-01989-5","DOIUrl":"10.1186/s40168-024-01989-5","url":null,"abstract":"<p><strong>Background: </strong>Biological invasions pose an escalating threat to native ecosystems. The accumulation of invasive alien plants worldwide is not saturated yet, underscoring the persistent and growing impact of invasions. Soil microorganisms play a key role in the process of alien plant invasion. However, the temporal dynamics of microbial communities has rarely been determined during the invasion owing to the dearth of long-term, in situ experimental systems.</p><p><strong>Results: </strong>Here, we examined the temporal succession of soil microbial communities 8 years after experiment setup in a common garden. Bacterial communities displayed divergent temporal succession, with invasive plants exhibiting higher turnover rates. Invasive alien plants reduced stochasticity in bacterial communities, likely acting as an environmental filter on community assembly. Plant growth-promoting microbes underwent higher succession rates in invasive alien plants compared to native plants, suggesting that invasive alien plants may possess a distinct advantage in fostering a favorable microbiota for their own growth and establishment. In sharp contrast, native plants selectively increased succession rates of specific plant pathogens. Furthermore, the microbial co-occurrence network was more complex in invasive plants, suggesting that invasive plants foster intricate relationships among microbial communities.</p><p><strong>Conclusions: </strong>Therefore, the asymmetric succession in soil microbial communities enables invasive plants recruit beneficial microbiota from the surrounding soil. These results deepen our understanding of the mechanism underlying plant invasion and provide novel insights into predicting the ecological consequences resulting from widespread plant invasion. This knowledge can be incorporated into management strategies to address the evolving challenges posed by invasive plants. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"265"},"PeriodicalIF":13.8,"publicationDate":"2024-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11662829/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142872536","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}