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Surface microlayer-mediated virome dissemination in the Central Arctic. 北极中部由表面微层介导的病毒传播。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s40168-024-01902-0
Janina Rahlff, George Westmeijer, Julia Weissenbach, Alfred Antson, Karin Holmfeldt

Background: Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited.

Results: To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2-5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations.

Conclusions: The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Video Abstract.

背景:水生病毒是形成微生物群落的关键角色。在极地环境中,它们面临着宿主有限和条件恶劣等重大挑战。然而,由于这些生态系统的可及性有限,我们对病毒多样性、丰度、适应性和宿主相互作用的了解仍然有限:为了填补这一知识空白,我们研究了北极中部和格陵兰岛北部与大气接近的水生生态系统中的病毒。在北极夏季奥登号破冰船进行 2021 年北极综合考察期间,我们从约 60 厘米深的水域和亚毫米表面微层(SML)采集了用于病毒宿主分析的水生样本。水样取自熔池和开放水域,然后进行大小分馏过滤,再进行基因组分辨元基因组和培养研究。与开放水域相比,熔池中的原核生物多样性要低得多。熔池中的原核生物主要是黄杆菌和 Aquiluna sp.,后者的基因组相对较小,只有 1.2 Mb,具有利用磷酸乙酰转移酶-乙酸激酶途径产生 ATP 的代谢潜力。与开放水域相比,熔池中宿主部分(0.2-5 微米)的病毒多样性非常有限。在1154个病毒操作分类单元(vOTUs)(其中三分之二是预测的噬菌体)中,17.2%的病毒编码具有代谢功能的辅助代谢基因(AMGs)。一些 AMGs,如甘油-3-磷酸胞苷酸转移酶和类冰结合蛋白,可能为宿主提供低温保护。噬菌体通常与SML基因组相关,北极SML菌株Leeuwenhoekiella aequorea Arc30的两个新病毒属的活性噬菌体被诱导出来。我们发现有证据表明,与 ~60 厘米深度相比,SML 中的 vOTU 丰度与五个不同北极站的 vOTU 分布呈正相关:结论:研究结果表明,病毒采用了精心设计的策略,以在宿主有限的极端环境中生存。此外,我们的观察结果表明,紧邻的海气界面是病毒在北极中部分布的平台。视频摘要
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引用次数: 0
Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn's disease location. 元蛋白质组学揭示了根据克罗恩病发病部位饮食诱导的肠道微生物组功能变化。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-23 DOI: 10.1186/s40168-024-01927-5
Stefano Levi Mortera, Valeria Marzano, Federica Rapisarda, Chiara Marangelo, Ilaria Pirona, Pamela Vernocchi, Marta Di Michele, Federica Del Chierico, Maria A Quintero, Irina Fernandez, Hajar Hazime, Rose M Killian, Norma Solis, Mailenys Ortega, Oriana M Damas, Siobhan Proksell, David H Kerman, Amar R Deshpande, Luis Garces, Franco Scaldaferri, Antonio Gasbarrini, Maria T Abreu, Lorenza Putignani

Background: Crohn's disease (CD) is characterized by chronic intestinal inflammation. Diet is a key modifiable factor influencing the gut microbiome (GM) and a risk factor for CD. However, the impact of diet modulation on GM function in CD patients is understudied. Herein, we evaluated the effect of a high-fiber, low-fat diet (the Mi-IBD diet) on GM function in CD patients. All participants were instructed to follow the Mi-IBD diet for 8 weeks. One group of CD patients received one-time diet counseling only (Gr1); catered food was supplied for the other three groups, including CD patients (Gr2) and dyads of CD patients and healthy household controls (HHCs) residing within the same household (Gr3-HHC dyads). Stool samples were collected at baseline, week 8, and week 36, and analyzed by liquid chromatography-tandem mass spectrometry.

Results: At baseline, the metaproteomic profiles of CD patients and HHCs differed. The Mi-IBD diet significantly increased carbohydrate and iron transport and metabolism. The predicted microbial composition underlying the metaproteomic changes differed between patients with ileal only disease (ICD) or colonic involvement: ICD was characterized by decreased Faecalibacterium abundance. Even on the Mi-IBD diet, the CD patient metaproteome displayed significant underrepresentation of carbohydrate and purine/pyrimidine synthesis pathways compared to that of HHCs. Human immune-related proteins were upregulated in CD patients compared to HHCs.

Conclusions: The Mi-IBD diet changed the microbial function of CD patients and enhanced carbohydrate metabolism. Our metaproteomic results highlight functional differences in the microbiome according to disease location. Notably, our dietary intervention yielded the most benefit for CD patients with colonic involvement compared to ileal-only disease. Video Abstract.

背景:克罗恩病(CD)以慢性肠道炎症为特征。饮食是影响肠道微生物组(GM)的一个关键可调节因素,也是克罗恩病的一个危险因素。然而,饮食调节对 CD 患者肠道微生物组功能的影响尚未得到充分研究。在此,我们评估了高纤维、低脂肪饮食(Mi-IBD 饮食)对 CD 患者肠道微生物组功能的影响。所有参与者都被要求遵循 Mi-IBD 饮食 8 周。其中一组 CD 患者只接受一次性饮食指导(Gr1);其他三组包括 CD 患者(Gr2)和居住在同一家庭中的 CD 患者和健康家庭对照组(HHCs)(Gr3-HHC dyads)。在基线、第8周和第36周收集粪便样本,并采用液相色谱-串联质谱法进行分析:结果:基线时,CD 患者和 HHC 的元蛋白组图谱不同。Mi-IBD饮食明显增加了碳水化合物和铁的转运和代谢。回肠疾病(ICD)或结肠受累患者的元蛋白组变化所依据的微生物组成预测不同:回肠疾病患者的粪便杆菌丰度降低。即使使用 Mi-IBD 饮食,CD 患者元蛋白质组中碳水化合物和嘌呤/嘧啶合成途径的代表性也明显低于 HHCs。与HHCs相比,CD患者的人类免疫相关蛋白上调:结论:Mi-IBD饮食改变了CD患者的微生物功能,促进了碳水化合物代谢。我们的元蛋白组学结果凸显了不同疾病部位微生物组的功能差异。值得注意的是,与单纯回肠疾病相比,我们的饮食干预对结肠受累的 CD 患者最有益。视频摘要。
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引用次数: 0
Fecal microbiota transplantation alters the proteomic landscape of inflammation in HIV: identifying bacterial drivers. 粪便微生物群移植改变了艾滋病病毒炎症的蛋白质组景观:确定细菌驱动因素。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 DOI: 10.1186/s40168-024-01919-5
Claudio Díaz-García, Elena Moreno, Alba Talavera-Rodríguez, Lucía Martín-Fernández, Sara González-Bodí, Laura Martín-Pedraza, José A Pérez-Molina, Fernando Dronda, María José Gosalbes, Laura Luna, María Jesús Vivancos, Jaime Huerta-Cepas, Santiago Moreno, Sergio Serrano-Villar

Background: Despite effective antiretroviral therapy, people with HIV (PWH) experience persistent systemic inflammation and increased morbidity and mortality. Modulating the gut microbiome through fecal microbiota transplantation (FMT) represents a novel therapeutic strategy. We aimed to evaluate proteomic changes in inflammatory pathways following repeated, low-dose FMT versus placebo.

Methods: This double-masked, placebo-controlled pilot study assessed the proteomic impacts of weekly FMT versus placebo treatment over 8 weeks on systemic inflammation in 29 PWH receiving stable antiretroviral therapy (ART). Three stool donors with high Faecalibacterium and butyrate profiles were selected, and their individual stools were used for FMT capsule preparation. Proteomic changes in 345 inflammatory proteins in plasma were quantified using the proximity extension assay, with samples collected at baseline and at weeks 1, 8, and 24. Concurrently, we characterized shifts in the gut microbiota composition and annotated functions through shotgun metagenomics. We fitted generalized additive models to evaluate the dynamics of protein expression. We selected the most relevant proteins to explore their correlations with microbiome composition and functionality over time using linear mixed models.

Results: FMT significantly reduced the plasma levels of 45 inflammatory proteins, including established mortality predictors such as IL6 and TNF-α. We found notable reductions persisting up to 16 weeks after the final FMT procedure, including in the expression of proteins such as CCL20 and CD22. We identified changes in 46 proteins, including decreases in FT3LG, IL6, IL10RB, IL12B, and IL17A, which correlated with multiple bacterial species. We found that specific bacterial species within the Ruminococcaceae, Succinivibrionaceae, Prevotellaceae families, and the Clostridium genus, in addition to their associated genes and functions, were significantly correlated with changes in inflammatory markers.

Conclusions: Targeting the gut microbiome through FMT effectively decreased inflammatory proteins in PWH, with sustained effects. These findings suggest the potential of the microbiome as a therapeutic target to mitigate inflammation-related complications in this population, encouraging further research and development of microbiome-based interventions. Video Abstract.

背景:尽管抗逆转录病毒疗法有效,但艾滋病病毒感染者(PWH)仍会出现持续的全身炎症,发病率和死亡率也会增加。通过粪便微生物群移植(FMT)调节肠道微生物群是一种新的治疗策略。我们的目的是评估反复低剂量 FMT 与安慰剂对比后炎症通路的蛋白质组变化:这项双掩蔽、安慰剂对照试验研究评估了 29 名接受稳定抗逆转录病毒疗法(ART)的感染者在接受为期 8 周的每周 FMT 与安慰剂治疗后,蛋白质组对全身炎症的影响。研究人员选择了三位粪便细菌和丁酸盐含量较高的粪便捐献者,并将他们的粪便用于 FMT 胶囊的制备。在基线期、第 1 周、第 8 周和第 24 周收集的样本中,使用近距离延伸测定法量化了血浆中 345 种炎症蛋白的蛋白质组变化。同时,我们还通过散弹枪元基因组学分析了肠道微生物群组成的变化和功能注释。我们拟合了广义加性模型来评估蛋白质表达的动态变化。我们选择了最相关的蛋白质,使用线性混合模型探讨它们与微生物群组成和功能随时间变化的相关性:结果:FMT 能明显降低 45 种炎症蛋白的血浆水平,包括 IL6 和 TNF-α 等已确定的死亡率预测因子。我们发现,在最后一次 FMT 过程结束后的 16 周内,包括 CCL20 和 CD22 等蛋白的表达在内的炎症蛋白水平仍有明显下降。我们发现了46种蛋白质的变化,包括FT3LG、IL6、IL10RB、IL12B和IL17A的减少,这与多种细菌种类有关。我们发现,反刍球菌科、琥珀酰菌科、普雷沃特菌科和梭菌属中的特定细菌种类及其相关基因和功能与炎症标志物的变化显著相关:结论:通过 FMT 以肠道微生物组为靶点,可有效降低 PWH 的炎症蛋白,且效果持久。这些研究结果表明,微生物组有可能成为减轻该人群炎症相关并发症的治疗靶点,从而鼓励人们进一步研究和开发基于微生物组的干预措施。视频摘要。
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引用次数: 0
Anaerostipes caccae CML199 enhances bone development and counteracts aging-induced bone loss through the butyrate-driven gut-bone axis: the chicken model. Anaerostipes caccae CML199通过丁酸驱动的肠道-骨骼轴促进骨骼发育并抵消衰老引起的骨质流失:鸡模型。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 DOI: 10.1186/s40168-024-01920-y
Zhengtian Lyu, Gaoxiang Yuan, Yuying Zhang, Fengwenhui Zhang, Yan Liu, Yifan Li, Guang Li, Ying Wang, Ming Zhang, Yongfei Hu, Yuming Guo, Dan Liu

Background: The gut microbiota is a key regulator of bone metabolism. Investigating the relationship between the gut microbiota and bone remodeling has revealed new avenues for the treatment of bone-related disorders. Despite significant progress in understanding gut microbiota-bone interactions in mammals, research on avian species remains limited. Birds have unique bone anatomy and physiology to support egg-laying. However, whether and how the gut microbiota affects bone physiology in birds is still unknown. In this study, we utilized laying hens as a research model to analyze bone development patterns, elucidate the relationships between bone and the gut microbiota, and mine probiotics with osteomodulatory effects.

Results: Aging led to a continuous increase in bone mineral density in the femur of laying hens. The continuous deposition of medullary bone in the bone marrow cavity of aged laying hens led to significant trabecular bone loss and weakened bone metabolism. The cecal microbial composition significantly shifted before and after sexual maturity, with some genera within the class Clostridia potentially linked to postnatal bone development in laying hens. Four bacterial strains associated with bone development, namely Blautia coccoides CML164, Fournierella sp002159185 CML151, Anaerostipes caccae CML199 (ANA), and Romboutsia lituseburensis CML137, were identified and assessed in chicks with low bacterial loads and chicken primary osteoblasts. Among these, ANA demonstrated the most significant promotion of bone formation both in vivo and in vitro, primarily attributed to butyrate in its fermentation products. A long-term feeding experiment of up to 72 weeks confirmed that ANA enhanced bone development during sexual maturity by improving the immune microenvironment of the bone marrow in laying hens. Dietary supplementation of ANA for 50 weeks prevented excessive medullary bone deposition and mitigated aging-induced trabecular bone loss.

Conclusions: These findings highlight the beneficial effects of ANA on bone physiology, offering new perspectives for microbial-based interventions for bone-related disorders in both poultry and possibly extending to human health. Video Abstract.

背景:肠道微生物群是骨代谢的关键调节因子。研究肠道微生物群与骨骼重塑之间的关系为治疗骨骼相关疾病提供了新途径。尽管在了解哺乳动物肠道微生物群与骨骼相互作用方面取得了重大进展,但对鸟类物种的研究仍然有限。鸟类具有独特的骨骼解剖和生理结构,以支持产蛋。然而,肠道微生物群是否以及如何影响鸟类的骨骼生理机能仍是未知数。在这项研究中,我们利用蛋鸡作为研究模型,分析骨骼发育模式,阐明骨骼与肠道微生物群之间的关系,并挖掘具有骨调节作用的益生菌:结果:衰老导致蛋鸡股骨中的骨矿物质密度持续增加。老龄蛋鸡骨髓腔中髓质骨的持续沉积导致骨小梁显著流失和骨代谢减弱。性成熟前后盲肠微生物组成发生了显著变化,梭菌属中的一些菌属可能与蛋鸡出生后的骨骼发育有关。在细菌负荷较低的雏鸡和鸡初级成骨细胞中鉴定并评估了与骨骼发育相关的四种细菌菌株,即Blautia coccoides CML164、Fournierella sp002159185 CML151、Anaerostipes caccae CML199(ANA)和Romboutsia lituseburensis CML137。其中,ANA 对体内和体外骨形成的促进作用最为显著,这主要归功于其发酵产物中的丁酸盐。一项长达 72 周的长期饲喂实验证实,ANA 通过改善蛋鸡骨髓的免疫微环境,促进了性成熟期间的骨骼发育。连续 50 周膳食补充 ANA 可防止髓质骨过度沉积,并减轻衰老引起的小梁骨质流失:这些发现强调了 ANA 对骨生理学的有益影响,为基于微生物的家禽骨相关疾病干预提供了新的视角,并可能扩展到人类健康。视频摘要。
{"title":"Anaerostipes caccae CML199 enhances bone development and counteracts aging-induced bone loss through the butyrate-driven gut-bone axis: the chicken model.","authors":"Zhengtian Lyu, Gaoxiang Yuan, Yuying Zhang, Fengwenhui Zhang, Yan Liu, Yifan Li, Guang Li, Ying Wang, Ming Zhang, Yongfei Hu, Yuming Guo, Dan Liu","doi":"10.1186/s40168-024-01920-y","DOIUrl":"https://doi.org/10.1186/s40168-024-01920-y","url":null,"abstract":"<p><strong>Background: </strong>The gut microbiota is a key regulator of bone metabolism. Investigating the relationship between the gut microbiota and bone remodeling has revealed new avenues for the treatment of bone-related disorders. Despite significant progress in understanding gut microbiota-bone interactions in mammals, research on avian species remains limited. Birds have unique bone anatomy and physiology to support egg-laying. However, whether and how the gut microbiota affects bone physiology in birds is still unknown. In this study, we utilized laying hens as a research model to analyze bone development patterns, elucidate the relationships between bone and the gut microbiota, and mine probiotics with osteomodulatory effects.</p><p><strong>Results: </strong>Aging led to a continuous increase in bone mineral density in the femur of laying hens. The continuous deposition of medullary bone in the bone marrow cavity of aged laying hens led to significant trabecular bone loss and weakened bone metabolism. The cecal microbial composition significantly shifted before and after sexual maturity, with some genera within the class Clostridia potentially linked to postnatal bone development in laying hens. Four bacterial strains associated with bone development, namely Blautia coccoides CML164, Fournierella sp002159185 CML151, Anaerostipes caccae CML199 (ANA), and Romboutsia lituseburensis CML137, were identified and assessed in chicks with low bacterial loads and chicken primary osteoblasts. Among these, ANA demonstrated the most significant promotion of bone formation both in vivo and in vitro, primarily attributed to butyrate in its fermentation products. A long-term feeding experiment of up to 72 weeks confirmed that ANA enhanced bone development during sexual maturity by improving the immune microenvironment of the bone marrow in laying hens. Dietary supplementation of ANA for 50 weeks prevented excessive medullary bone deposition and mitigated aging-induced trabecular bone loss.</p><p><strong>Conclusions: </strong>These findings highlight the beneficial effects of ANA on bone physiology, offering new perspectives for microbial-based interventions for bone-related disorders in both poultry and possibly extending to human health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11495078/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503479","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}
引用次数: 0
Maternal gastrointestinal microbiome shapes gut microbial function and resistome of newborns in a cow-to-calf model. 在母牛到小牛模型中,母体胃肠道微生物组影响新生儿的肠道微生物功能和抗性组。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 DOI: 10.1186/s40168-024-01943-5
Yimin Zhuang, Shuai Liu, Duo Gao, Yiming Xu, Wen Jiang, Guobin Hou, Sumin Li, Xinjie Zhao, Tianyu Chen, Shangru Li, Siyuan Zhang, Yanting Huang, Jingjun Wang, Jianxin Xiao, Mengmeng Li, Wei Wang, Shengli Li, Zhijun Cao

Background: The maternal gut microbiome is the direct and important source of early colonization and development of the neonatal gut microbiome. However, differences in unique and shared features between mothers with different physiological phenotypes and their newborns still lack exhaustive investigation. Here, using a cow-to-calf model, a comprehensive investigation was conducted to elucidate the pattern and characterization of microbial transfer from the maternal source to the offspring.

Results: The microbiota in the rumen and feces of dairy cows were divided into two clusters via enterotype analysis. The cows from the enterotype distinguished by Prevotella in the rumen had better production performance, whereas no difference was observed in the cows classified by feces enterotype. Furthermore, through a pairwise combination of fecal and ruminal enterotypes, we screened a group of dairy cows with excellent phenotypes. The gastrointestinal microbiomes of cows with different phenotypes and their offspring differed significantly. The rumen was a more important microbial source for meconium than feces. Transmission of beneficial bacteria from mother to offspring was observed. Additionally, the meconium inherits advantageous metabolic functions of the rumen. The resistome features of the rumen, feces, and meconium were consistent, and resistome abundance from cows to calves showed an expanding trend. The interaction between antibiotic-resistance genes and mobile genetic elements from the rumen to meconium was the most remarkable. The diversity of core metabolites from cows to calves was stable and not affected by differences in phenotypes. However, the abundance of specific metabolites varied greatly.

Conclusions: Our study demonstrates the microbial taxa, metabolic function, and resistome characteristics of maternal and neonatal microbiomes, and reveals the potential vertical transmission of the microbiome from a cow-to-calf model. These findings provide new insights into the transgenerational transmission pattern of the microbiome. Video Abstract.

背景:母体肠道微生物组是新生儿肠道微生物组早期定植和发育的直接和重要来源。然而,对不同生理表型的母亲及其新生儿之间的独特和共同特征的差异仍缺乏详尽的研究。在此,我们利用母牛到小牛的模型进行了全面调查,以阐明微生物从母源向子代转移的模式和特征:结果:通过肠型分析,奶牛瘤胃和粪便中的微生物群被分为两组。根据瘤胃中的普雷沃特氏菌区分的肠型奶牛生产性能更好,而根据粪便肠型划分的奶牛则无差异。此外,通过粪便肠型和瘤胃肠型的配对组合,我们筛选出了一组表型优异的奶牛。不同表型奶牛及其后代的胃肠道微生物组存在显著差异。与粪便相比,瘤胃是胎粪更重要的微生物来源。观察到有益菌从母体传播给后代。此外,胎粪还继承了瘤胃的优势代谢功能。瘤胃、粪便和胎粪的耐药性组特征是一致的,从奶牛到犊牛的耐药性组丰度呈扩大趋势。从瘤胃到胎粪,抗生素耐药性基因与移动遗传因子之间的相互作用最为显著。从奶牛到犊牛,核心代谢物的多样性是稳定的,不受表型差异的影响。然而,特定代谢物的丰度差异很大:我们的研究展示了母体和新生儿微生物组的微生物类群、代谢功能和抗性组特征,并揭示了微生物组从母牛到小牛模型的潜在垂直传播。这些发现为微生物组的跨代传播模式提供了新的见解。视频摘要。
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引用次数: 0
The Staphylococcus aureus-antagonizing human nasal commensal Staphylococcus lugdunensis depends on siderophore piracy. 可拮抗金黄色葡萄球菌的人类鼻腔共生葡萄球菌卢格敦金黄色葡萄球菌依赖于嗜苷酸盐海盗。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 DOI: 10.1186/s40168-024-01913-x
Ralf Rosenstein, Benjamin O Torres Salazar, Claudia Sauer, Simon Heilbronner, Bernhard Krismer, Andreas Peschel

Background: Bacterial pathogens such as Staphylococcus aureus colonize body surfaces of part of the human population, which represents a critical risk factor for skin disorders and invasive infections. However, such pathogens do not belong to the human core microbiomes. Beneficial commensal bacteria can often prevent the invasion and persistence of such pathogens by using molecular strategies that are only superficially understood. We recently reported that the commensal bacterium Staphylococcus lugdunensis produces the novel antibiotic lugdunin, which eradicates S. aureus from the nasal microbiomes of hospitalized patients. However, it has remained unclear if S. lugdunensis may affect S. aureus carriage in the general population and which external factors might promote S. lugdunensis carriage to enhance its S. aureus-eliminating capacity.

Results: We could cultivate S. lugdunensis from the noses of 6.3% of healthy human volunteers. In addition, S. lugdunensis DNA could be identified in metagenomes of many culture-negative nasal samples indicating that cultivation success depends on a specific bacterial threshold density. Healthy S. lugdunensis carriers had a 5.2-fold lower propensity to be colonized by S. aureus indicating that lugdunin can eliminate S. aureus also in healthy humans. S. lugdunensis-positive microbiomes were dominated by either Staphylococcus epidermidis, Corynebacterium species, or Dolosigranulum pigrum. These and further bacterial commensals, whose abundance was positively associated with S. lugdunensis, promoted S. lugdunensis growth in co-culture. Such mutualistic interactions depended on the production of iron-scavenging siderophores by supportive commensals and on the capacity of S. lugdunensis to import siderophores. Video Abstract CONCLUSIONS: These findings underscore the importance of microbiome homeostasis for eliminating pathogen colonization. Elucidating mechanisms that drive microbiome interactions will become crucial for microbiome-precision editing approaches.

背景:金黄色葡萄球菌等细菌病原体定植于部分人群的体表,是导致皮肤病和侵入性感染的重要风险因素。然而,这类病原体并不属于人类核心微生物组。有益的共生细菌通常可以利用分子策略阻止这类病原体的入侵和持续存在,但人们对这些策略的了解还很肤浅。我们最近报告说,共生细菌卢格杜恩葡萄球菌能产生新型抗生素卢格杜宁,它能根除住院患者鼻腔微生物组中的金黄色葡萄球菌。然而,目前仍不清楚卢格杜菌是否会影响普通人群中的金黄色葡萄球菌携带,以及哪些外部因素可能会促进卢格杜菌的携带,从而增强其消灭金黄色葡萄球菌的能力:结果:我们可以从 6.3% 的健康志愿者鼻腔中培养出卢格登氏菌。此外,在许多培养阴性的鼻腔样本的元基因组中可以鉴定出 S. lugdunensis DNA,这表明培养成功与否取决于特定的细菌阈值密度。健康的 S. lugdunensis 携带者被金黄色葡萄球菌定植的可能性降低了 5.2 倍,这表明 lugdunin 也能消灭健康人体内的金黄色葡萄球菌。卢格杜氏菌阳性微生物组主要由表皮葡萄球菌、棒状杆菌或猪多糖所组成。这些细菌和其他细菌共生体(其丰度与 S. lugdunensis 呈正相关)在共培养中促进了 S. lugdunensis 的生长。这种互利的相互作用取决于支持性共生菌产生的铁清除嗜苷酸盐以及卢格氏菌输入嗜苷酸盐的能力。视频摘要 结论:这些发现强调了微生物组平衡对消除病原体定植的重要性。阐明驱动微生物组相互作用的机制将成为微生物组精确编辑方法的关键。
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引用次数: 0
Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation. 挥发性物质介导的植物种间相互作用通过诱导根部渗出的变化,促进有益细菌在根部定殖。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-21 DOI: 10.1186/s40168-024-01914-w
Xingang Zhou, Jingyu Zhang, Jibo Shi, Muhammad Khashi U Rahman, Hongwei Liu, Zhong Wei, Fengzhi Wu, Francisco Dini-Andreote

Background: Volatile organic compounds (VOCs) released by plants can act as signaling molecules mediating ecological interactions. Therefore, the study of VOCs mediated intra- and interspecific interactions with downstream plant physiological responses is critical to advance our understanding of mechanisms underlying information exchange in plants. Here, we investigated how plant-emitted VOCs affect the performance of an interspecific neighboring plant via induced shifts in root exudate chemistry with implications for root-associated microbiota recruitment.

Results: First, we showed that VOCs emitted by potato-onion plants stimulate the growth of adjacent tomato plants. Then, we demonstrated that this positive effect on tomato biomass was attributed to shifts in the tomato rhizosphere microbiota. Specifically, we found potato-onion VOCs to indirectly affect the recruitment of specific bacteria (e.g., Pseudomonas and Bacillus spp.) in the tomato rhizosphere. Second, we identified and validated the compound dipropyl disulfide as the active molecule within the blend of potato-onion VOCs mediating this interspecific plant communication. Third, we showed that the effect on the tomato rhizosphere microbiota occurs via induced changes in root exudates of tomato plants caused by exposure to dipropyl disulfide. Last, Pseudomonas and Bacillus spp. bacteria enriched in the tomato rhizosphere were shown to have plant growth-promoting activities.

Conclusions: Potato-onion VOCs-specifically dipropyl disulfide-can induce shifts in the root exudate of adjacent tomato plants, which results in the recruitment of plant-beneficial bacteria in the rhizosphere. Taken together, this study elucidated a new mechanism of interspecific plant interaction mediated by VOCs resulting in alterations in the rhizosphere microbiota with beneficial outcomes for plant performance. Video Abstract.

背景:植物释放的挥发性有机化合物(VOCs)可作为介导生态相互作用的信号分子。因此,研究挥发性有机化合物介导的种内和种间相互作用以及下游植物生理反应,对于加深我们对植物信息交流机制的理解至关重要。在这里,我们研究了植物释放的挥发性有机化合物如何通过诱导根部渗出物化学变化影响种间相邻植物的表现,并对根相关微生物群的招募产生影响:结果:首先,我们发现马铃薯-洋葱植物释放的挥发性有机化合物会刺激相邻番茄植物的生长。然后,我们证明这种对番茄生物量的积极影响归因于番茄根瘤微生物群的变化。具体来说,我们发现马铃薯挥发性有机化合物会间接影响番茄根圈中特定细菌(如假单胞菌和芽孢杆菌属)的繁殖。其次,我们确定并验证了二丙基二硫化合物是马铃薯-洋葱挥发性有机化合物混合物中介导这种植物种间交流的活性分子。第三,我们发现,暴露于二丙基二硫化物会诱导番茄植株根部渗出物发生变化,从而对番茄根瘤微生物群产生影响。最后,番茄根圈中富集的假单胞菌和芽孢杆菌具有促进植物生长的活性:结论:马铃薯离子挥发性有机化合物(特别是二丙基二硫化物)可诱导相邻番茄植株根部渗出液的变化,从而导致根圈中有益于植物的细菌大量繁殖。综上所述,这项研究阐明了一种由挥发性有机化合物介导的植物种间相互作用的新机制,它导致根圈微生物群的改变,从而对植物的表现产生有益的结果。视频摘要。
{"title":"Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation.","authors":"Xingang Zhou, Jingyu Zhang, Jibo Shi, Muhammad Khashi U Rahman, Hongwei Liu, Zhong Wei, Fengzhi Wu, Francisco Dini-Andreote","doi":"10.1186/s40168-024-01914-w","DOIUrl":"10.1186/s40168-024-01914-w","url":null,"abstract":"<p><strong>Background: </strong>Volatile organic compounds (VOCs) released by plants can act as signaling molecules mediating ecological interactions. Therefore, the study of VOCs mediated intra- and interspecific interactions with downstream plant physiological responses is critical to advance our understanding of mechanisms underlying information exchange in plants. Here, we investigated how plant-emitted VOCs affect the performance of an interspecific neighboring plant via induced shifts in root exudate chemistry with implications for root-associated microbiota recruitment.</p><p><strong>Results: </strong>First, we showed that VOCs emitted by potato-onion plants stimulate the growth of adjacent tomato plants. Then, we demonstrated that this positive effect on tomato biomass was attributed to shifts in the tomato rhizosphere microbiota. Specifically, we found potato-onion VOCs to indirectly affect the recruitment of specific bacteria (e.g., Pseudomonas and Bacillus spp.) in the tomato rhizosphere. Second, we identified and validated the compound dipropyl disulfide as the active molecule within the blend of potato-onion VOCs mediating this interspecific plant communication. Third, we showed that the effect on the tomato rhizosphere microbiota occurs via induced changes in root exudates of tomato plants caused by exposure to dipropyl disulfide. Last, Pseudomonas and Bacillus spp. bacteria enriched in the tomato rhizosphere were shown to have plant growth-promoting activities.</p><p><strong>Conclusions: </strong>Potato-onion VOCs-specifically dipropyl disulfide-can induce shifts in the root exudate of adjacent tomato plants, which results in the recruitment of plant-beneficial bacteria in the rhizosphere. Taken together, this study elucidated a new mechanism of interspecific plant interaction mediated by VOCs resulting in alterations in the rhizosphere microbiota with beneficial outcomes for plant performance. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":null,"pages":null},"PeriodicalIF":13.8,"publicationDate":"2024-10-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11492557/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142469621","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}
引用次数: 0
Host-microbe interaction-mediated resistance to DSS-induced inflammatory enteritis in sheep. 宿主-微生物相互作用介导的绵羊对 DSS 诱导的炎症性肠炎的抵抗力。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-21 DOI: 10.1186/s40168-024-01932-8
Shuo Yan, Ruilin Du, Wenna Yao, Huimin Zhang, Yue Xue, Teligun, Yongfa Li, Hanggai Bao, Yulong Zhao, Shuo Cao, Guifang Cao, Xihe Li, Siqin Bao, Yongli Song

Background: The disease resistance phenotype is closely related to immunomodulatory function and immune tolerance and has far-reaching implications in animal husbandry and human health. Microbes play an important role in the initiation, prevention, and treatment of diseases, but the mechanisms of host-microbiota interactions in disease-resistant phenotypes are poorly understood. In this study, we hope to uncover and explain the role of microbes in intestinal diseases and their mechanisms of action to identify new potential treatments.

Methods: First, we established the colitis model of DSS in two breeds of sheep and then collected the samples for multi-omics testing including metagenes, metabolome, and transcriptome. Next, we made the fecal bacteria liquid from the four groups of sheep feces collected from H-CON, H-DSS, E-CON, and E-DSS to transplant the fecal bacteria into mice. H-CON feces were transplanted into mice named HH group and H-DSS feces were transplanted into mice named HD group and Roseburia bacteria treatment named HDR groups. E-CON feces were transplanted into mice named EH group and E-DSS feces were transplanted into mice in the ED group and Roseburia bacteria treatment named EDR groups. After successful modeling, samples were taken for multi-omics testing. Finally, colitis mice in HD group and ED group were administrated with Roseburia bacteria, and the treatment effect was evaluated by H&E, PAS, immunohistochemistry, and other experimental methods.

Results: The difference in disease resistance of sheep to DSS-induced colitis disease is mainly due to the increase in the abundance of Roseburia bacteria and the increase of bile acid secretion in the intestinal tract of Hu sheep in addition to the accumulation of potentially harmful bacteria in the intestine when the disease occurs, which makes the disease resistance of Hu sheep stronger under the same disease conditions. However, the enrichment of harmful microorganisms in East Friesian sheep activated the TNFα signalling pathway, which aggravated the intestinal injury, and then the treatment of FMT mice by culturing Roseburia bacteria found that Roseburia bacteria had a good curative effect on colitis.

Conclusion: Our study showed that in H-DSS-treated sheep, the intestinal barrier is stabilized with an increase in the abundance of beneficial microorganisms. Our data also suggest that Roseburia bacteria have a protective effect on the intestinal barrier of Hu sheep. Accumulating evidence suggests that host-microbiota interactions are associated with IBD disease progression. Video Abstract.

背景:抗病表型与免疫调节功能和免疫耐受密切相关,对畜牧业和人类健康具有深远影响。微生物在疾病的诱发、预防和治疗中发挥着重要作用,但宿主与微生物群在抗病表型中的相互作用机制却鲜为人知。在这项研究中,我们希望揭示和解释微生物在肠道疾病中的作用及其作用机制,从而找出新的潜在治疗方法:首先,我们在两个品种的绵羊中建立了 DSS 结肠炎模型,然后采集样本进行多组学检测,包括元基因组、代谢组和转录组。接着,我们将收集到的 H-CON、H-DSS、E-CON 和 E-DSS 四组绵羊粪便制成粪便菌液,将粪便菌移植到小鼠体内。H-CON粪便移植到小鼠体内命名为HH组,H-DSS粪便移植到小鼠体内命名为HD组,Roseburia细菌处理命名为HDR组。E-CON 粪便移植到 EH 组小鼠体内,E-DSS 粪便移植到 ED 组小鼠体内,Roseburia 细菌处理命名为 EDR 组。建模成功后,取样进行多组学检测。最后,给HD组和ED组的结肠炎小鼠注射罗斯布氏菌,并通过H&E、PAS、免疫组化等实验方法评价治疗效果:结果:绵羊对DSS诱导的结肠炎疾病的抗病力差异主要是由于胡羊肠道中罗斯布氏菌的丰度增加,胆汁酸分泌增加,此外,发病时肠道中潜在的有害细菌也会积累,这使得胡羊在相同的发病条件下抗病力更强。然而,东弗里斯兰羊体内有害微生物的富集激活了TNFα信号通路,加重了肠道损伤,再通过培养罗斯堡菌治疗FMT小鼠发现,罗斯堡菌对结肠炎有很好的治疗效果:我们的研究表明,经 H-DSS 处理的绵羊肠道屏障得到稳定,有益微生物数量增加。我们的数据还表明,Roseburia 菌对胡羊的肠道屏障具有保护作用。越来越多的证据表明,宿主与微生物群之间的相互作用与 IBD 疾病的进展有关。视频摘要。
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引用次数: 0
Xylanase enhances gut microbiota-derived butyrate to exert immune-protective effects in a histone deacetylase-dependent manner. 木聚糖酶以组蛋白去乙酰化酶依赖的方式增强肠道微生物群衍生的丁酸盐,从而发挥免疫保护作用。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-21 DOI: 10.1186/s40168-024-01934-6
Tong Wang, Nannan Zhou, Feifei Ding, Zhenzhen Hao, Jorge Galindo-Villegas, Zhenyu Du, Xiaoyun Su, Meiling Zhang

Background: Commensal bacteria in the intestine release enzymes to degrade and ferment dietary components, producing beneficial metabolites. However, the regulatory effects of microbial-derived enzymes on the intestinal microbiota composition and the influence on host health remain elusive. Xylanase can degrade xylan into oligosaccharides, showing wide application in feed industry.

Results: To validate the immune-protective effects of xylanase, Nile tilapia was used as the model and fed with xylanase. The results showed that dietary xylanase improved the survival rate of Nile tilapia when they were challenged with Aeromonas hydrophila. The transcriptome analysis showed significant enrichment of genes related to interleukin-17d (il-17d) signaling pathway in the xylanase treatment group. High-throughput sequencing revealed that dietary xylanase altered the composition of the intestinal microbiota and directly promoted the proliferation of Allobaculum stercoricanis which could produce butyrate in vitro. Consequently, dietary xylanase supplementation increased the butyrate level in fish gut. Further experiment verified that butyrate supplementation enhanced the expression of il-17d and regenerating islet-derived 3 gamma (reg3g) in the gut. The knockdown experiment of il-17d confirmed that il-17d is necessary for butyrate to protect Nile tilapia from pathogen resistance. Flow cytometry analysis indicated that butyrate increased the abundance of IL-17D+ intestinal epithelial cells in fish. Mechanistically, butyrate functions as an HDAC3 inhibitor, enhancing il-17d expression and playing a crucial role in pathogen resistance.

Conclusion: Dietary xylanase significantly altered the composition of intestinal microbiota and increased the content of butyrate in the intestine. Butyrate activated the transcription of il-17d in intestinal epithelial cells by inhibiting histone deacetylase 3, thereby protecting the Nile tilapia from pathogen infection. This study elucidated how microbial-derived xylanase regulates host immune function, providing a theoretical basis for the development and application of functional enzymes. Video Abstract.

背景:肠道中的共生细菌会释放酶来降解和发酵食物成分,产生有益的代谢物。然而,微生物衍生酶对肠道微生物群组成的调控作用以及对宿主健康的影响仍然难以捉摸。木聚糖酶可将木聚糖降解为低聚糖,在饲料行业有广泛应用:结果:为了验证木聚糖酶的免疫保护作用,以尼罗罗非鱼为模型,用木聚糖酶饲喂。结果表明,当尼罗罗非鱼受到嗜水气单胞菌挑战时,日粮中的木聚糖酶可提高其存活率。转录组分析表明,在木聚糖酶处理组中,与白细胞介素-17d(il-17d)信号通路相关的基因显著富集。高通量测序显示,膳食木聚糖酶改变了肠道微生物群的组成,并直接促进了可在体外产生丁酸的Allobaculum stercoricanis的增殖。因此,膳食中添加木聚糖酶可提高鱼类肠道中的丁酸盐含量。进一步的实验证实,补充丁酸盐可提高肠道中 il-17d 和再生胰岛衍生 3 γ(reg3g)的表达。il-17d的敲除实验证实,il-17d是丁酸盐保护尼罗罗非鱼抵抗病原体的必要条件。流式细胞术分析表明,丁酸盐增加了鱼体内IL-17D+肠上皮细胞的丰度。从机理上讲,丁酸盐是一种 HDAC3 抑制剂,可提高 IL-17d 的表达,在抗病原体中发挥重要作用:结论:膳食木聚糖酶显著改变了肠道微生物群的组成,增加了肠道中丁酸盐的含量。丁酸盐通过抑制组蛋白去乙酰化酶 3 激活肠上皮细胞中 il-17d 的转录,从而保护尼罗罗非鱼免受病原体感染。这项研究阐明了微生物衍生的木聚糖酶如何调节宿主免疫功能,为功能酶的开发和应用提供了理论依据。视频摘要。
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引用次数: 0
Balancing the scales: assessing the impact of irrigation and pathogen burden on potato blackleg disease and soil microbial communities. 平衡天平:评估灌溉和病原体负担对马铃薯黑胫病和土壤微生物群落的影响。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-21 DOI: 10.1186/s40168-024-01918-6
Ciara Keating, Elizabeth Kilbride, Mark A Stalham, Charlotte Nellist, Joel Milner, Sonia Humphris, Ian Toth, Barbara K Mable, Umer Zeeshan Ijaz

Background: Understanding the interaction between environmental conditions, crop yields, and soil health is crucial for sustainable agriculture in a changing climate. Management practices to limit disease are a balancing act. For example, in potato production, dry conditions favour common scab (Streptomyces spp.) and wet conditions favour blackleg disease (Pectobacterium spp.). The exact mechanisms involved and how these link to changes in the soil microbiome are unclear. Our objectives were to test how irrigation management and bacterial pathogen load in potato seed stocks impact: (i) crop yields; (ii) disease development (blackleg or common scab); and (iii) soil microbial community dynamics.

Methods: We used stocks of seed potatoes with varying natural levels of Pectobacterium (Jelly [high load], Jelly [low load] and Estima [Zero - no Pectobacterium]). Stocks were grown under four irrigation regimes that differed in the timing and level of watering. The soil microbial communities were profiled using amplicon sequencing at 50% plant emergence and at harvest. Generalised linear latent variable models and an annotation-free mathematical framework approach (ensemble quotient analysis) were then used to show the interacting microbes with irrigation regime and Pectobacterium pathogen levels.

Results: Irrigation increased blackleg symptoms in the plots planted with stocks with low and high levels of Pectobacterium (22-34%) but not in the zero stock (2-6%). However, withholding irrigation increased common scab symptoms (2-5%) and reduced crop yields. Irrigation did not impact the composition of the soil microbiome, but planting stock with a high Pectobacterium burden resulted in an increased abundance of Planctomycetota, Anaerolinea and Acidobacteria species within the microbiome. Ensemble quotient analysis highlighted the Anaerolinea taxa were highly associated with high levels of Pectobacterium in the seed stock and blackleg symptoms in the field.

Conclusions: We conclude that planting seed stocks with a high Pectobacterium burden alters the abundance of specific microbial species within the soil microbiome and suggest that managing pathogen load in seed stocks could substantially affect soil communities, affecting crop health and productivity. Video Abstract.

背景:了解环境条件、作物产量和土壤健康之间的相互作用,对于在不断变化的气候条件下实现可持续农业至关重要。限制病害的管理措施是一种平衡行为。例如,在马铃薯生产中,干燥的条件有利于普通疮痂病(链霉菌属),而潮湿的条件则有利于黑胫病(果胶杆菌属)。其中涉及的确切机制以及这些机制如何与土壤微生物组的变化联系起来尚不清楚。我们的目标是测试马铃薯种群的灌溉管理和细菌病原体负荷如何影响:(i) 作物产量;(ii) 病害发展(黑腿病或普通疮痂病);以及 (iii) 土壤微生物群落动态:我们使用了果胶细菌天然含量不同的马铃薯种薯(Jelly [高负载]、Jelly [低负载] 和 Estima [零-无果胶细菌])。种薯在四种不同的灌溉制度下生长,灌溉的时间和程度各不相同。在 50%植株出苗时和收获时,使用扩增子测序分析土壤微生物群落。然后使用广义线性潜变量模型和无注释数学框架方法(集合商分析)来显示微生物与灌溉制度和果胶杆菌病原体水平之间的相互作用:结果:灌溉增加了种植果胶杆菌含量低和高的种群(22%-34%)的地块的黑胫病症状,但没有增加零种群(2%-6%)的地块的黑胫病症状。然而,停止灌溉会增加常见的疮痂病症状(2-5%)并降低作物产量。灌溉并不影响土壤微生物组的组成,但种植果胶杆菌含量高的种群会导致微生物组中的扁孢菌属、厌氧菌属和酸性菌属物种数量增加。集合商数分析表明,Anaerolinea类群与种群中果胶细菌含量高和田间黑腿症状高度相关:我们得出的结论是,种植果胶杆菌含量高的种群会改变土壤微生物组中特定微生物物种的丰度,并表明管理种群中的病原体负荷会对土壤群落产生重大影响,从而影响作物的健康和产量。视频摘要。
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