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Deep mutation, insertion and deletion scanning across the Enterovirus A proteome reveals constraints shaping viral evolution 对 A 型肠病毒蛋白质组进行深度突变、插入和缺失扫描,揭示影响病毒进化的制约因素
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-28 DOI: 10.1038/s41564-024-01871-y
William Bakhache, Walker Symonds-Orr, Lauren McCormick, Patrick T. Dolan
Insertions and deletions (InDels) are essential to protein evolution. In RNA viruses, InDels contribute to the emergence of viruses with new phenotypes, including altered host engagement and tropism. However, the tolerance of viral proteins for InDels has not been extensively studied. Here, we conduct deep mutational scanning to map and quantify the mutational tolerance of a complete viral proteome to insertion, deletion and substitution. We engineered approximately 45,000 insertions, 6,000 deletions and 41,000 amino acid substitutions across the nearly 2,200 coding positions of the Enterovirus A71 proteome, quantifying their effects on viral fitness by population sequencing. The vast majority of InDels are lethal to the virus, tolerated at only a few hotspots. Some of these hotspots overlap with sites of host recognition and immune engagement, suggesting tolerance at these sites reflects the important role InDels have played in the past phenotypic diversification of Enterovirus A. Deep mutational scanning of Enterovirus A71 maps and quantifies the impact of genomic insertions, deletions and substitutions on virus fitness and highlights the role of insertions and deletions in the diversification of RNA viruses.
插入和缺失(InDels)对蛋白质进化至关重要。在 RNA 病毒中,InDels 有助于病毒产生新的表型,包括改变宿主参与和滋养性。然而,病毒蛋白质对 InDels 的耐受性尚未得到广泛研究。在这里,我们进行了深度突变扫描,以绘制和量化完整病毒蛋白质组对插入、缺失和置换的突变耐受性。我们在肠病毒 A71 蛋白组的近 2,200 个编码位置上设计了约 45,000 个插入位、6,000 个缺失位和 41,000 个氨基酸替换位,并通过群体测序量化了它们对病毒适应性的影响。绝大多数 InDels 对病毒都是致命的,只有少数几个热点可以容忍。其中一些热点与宿主识别和免疫参与位点重叠,表明这些位点的耐受性反映了 InDels 在肠病毒 A 过去的表型多样化过程中发挥的重要作用。
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引用次数: 0
A year of microbiology 微生物学年
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-27 DOI: 10.1038/s41564-024-01880-x
We look back at this year’s Nature Microbiology content covering the spectrum of microbiology, from fundamental advances to those that aim to tackle pressing concerns facing human health, the environment and the climate.
我们回顾了今年《自然-微生物学》的内容,涵盖了微生物学的各个领域,从基础研究进展到旨在解决人类健康、环境和气候面临的紧迫问题的研究。
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引用次数: 0
Gut physiology and environment explain variations in human gut microbiome composition and metabolism 肠道生理学和环境可解释人类肠道微生物群组成和代谢的变化
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-27 DOI: 10.1038/s41564-024-01856-x
Nicola Procházková, Martin F. Laursen, Giorgia La Barbera, Eirini Tsekitsidi, Malte S. Jørgensen, Morten A. Rasmussen, Jeroen Raes, Tine R. Licht, Lars O. Dragsted, Henrik M. Roager
The human gut microbiome is highly personal. However, the contribution of gut physiology and environment to variations in the gut microbiome remains understudied. Here we performed an observational trial using multi-omics to profile microbiome composition and metabolism in 61 healthy adults for 9 consecutive days. We assessed day-to-day changes in gut environmental factors and measured whole-gut and segmental intestinal transit time and pH using a wireless motility capsule in a subset of 50 individuals. We observed substantial daily fluctuations, with intra-individual variations in gut microbiome and metabolism associated with changes in stool moisture and faecal pH, and inter-individual variations accounted for by whole-gut and segmental transit times and pH. Metabolites derived from microbial carbohydrate fermentation correlated negatively with the gut passage time and pH, while proteolytic metabolites and breath methane showed a positive correlation. Finally, we identified associations between segmental transit time/pH and coffee-, diet-, host- and microbial-derived metabolites. Our work suggests that gut physiology and environment are key to understanding the individuality of the human gut microbial composition and metabolism. An observational longitudinal clinical trial, incorporating a SmartPill and metabolomics, reveals the role of host factors in shaping the gut microbiome in healthy human adults.
人类肠道微生物组是高度个性化的。然而,肠道生理和环境对肠道微生物组变化的影响仍未得到充分研究。在此,我们进行了一项观察性试验,利用多组学技术对 61 名健康成年人连续 9 天的微生物组组成和代谢情况进行了分析。我们评估了肠道环境因素的逐日变化,并使用无线蠕动胶囊测量了 50 人的全肠和节段肠道转运时间和 pH 值。我们观察到每天都有很大的波动,个体内肠道微生物群和新陈代谢的变化与粪便水分和粪便 pH 值的变化有关,而个体间的变化则由全肠和节段性肠道转运时间和 pH 值决定。微生物碳水化合物发酵产生的代谢物与肠道通过时间和 pH 值呈负相关,而蛋白水解代谢物和呼出甲烷呈正相关。最后,我们确定了节段通过时间/pH 与咖啡、饮食、宿主和微生物衍生代谢物之间的关联。我们的研究表明,肠道生理和环境是了解人类肠道微生物组成和新陈代谢个性的关键。
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引用次数: 0
A framework for understanding collective microbiome metabolism 了解微生物群集体代谢的框架
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-26 DOI: 10.1038/s41564-024-01850-3
Matthias Huelsmann, Olga T. Schubert, Martin Ackermann
Microbiome metabolism underlies numerous vital ecosystem functions. Individual microbiome members often perform partial catabolism of substrates or do not express all of the metabolic functions required for growth. Microbiome members can complement each other by exchanging metabolic intermediates and cellular building blocks to achieve a collective metabolism. We currently lack a mechanistic framework to explain why microbiome members adopt partial metabolism and how metabolic functions are distributed among them. Here we argue that natural selection for proteome efficiency—that is, performing essential metabolic fluxes at a minimal protein investment—explains partial metabolism of microbiome members, which underpins the collective metabolism of microbiomes. Using the carbon cycle as an example, we discuss motifs of collective metabolism, the conditions under which these motifs increase the proteome efficiency of individuals and the metabolic interactions they result in. In summary, we propose a mechanistic framework for how collective metabolic functions emerge from selection on individuals. This Perspective explores why microbiome members perform partial metabolism of substrates and suggests that proteome efficiency is a driver of collective microbiome metabolism.
微生物组的新陈代谢是众多重要生态系统功能的基础。单个微生物群成员通常会对底物进行部分分解代谢,或不表达生长所需的全部代谢功能。微生物群成员可以通过交换代谢中间产物和细胞构筑物来实现集体代谢,从而实现互补。目前,我们缺乏一个机制框架来解释微生物组成员为何采用部分代谢以及代谢功能如何在它们之间分配。在这里,我们认为蛋白质组效率的自然选择--即以最小的蛋白质投资来完成必要的代谢通量--解释了微生物组成员的部分代谢,这也是微生物组集体代谢的基础。以碳循环为例,我们讨论了集体新陈代谢的模式、这些模式提高个体蛋白质组效率的条件以及它们导致的新陈代谢相互作用。总之,我们提出了一个机制框架,说明个体选择如何产生集体代谢功能。
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引用次数: 0
Retraction Note: Culture of previously uncultured members of the human gut microbiota by culturomics 撤稿说明:通过培养组学培养以前未培养的人类肠道微生物群成员
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-22 DOI: 10.1038/s41564-024-01894-5
Jean-Christophe Lagier, Saber Khelaifia, Maryam Tidjani Alou, Sokhna Ndongo, Niokhor Dione, Perrine Hugon, Aurelia Caputo, Frédéric Cadoret, Sory Ibrahima Traore, El Hadji Seck, Gregory Dubourg, Guillaume Durand, Gaël Mourembou, Elodie Guilhot, Amadou Togo, Sara Bellali, Dipankar Bachar, Nadim Cassir, Fadi Bittar, Jérémy Delerce, Morgane Mailhe, Davide Ricaboni, Melhem Bilen, Nicole Prisca Makaya Dangui Nieko, Ndeye Mery Dia Badiane, Camille Valles, Donia Mouelhi, Khoudia Diop, Matthieu Million, Didier Musso, Jônatas Abrahão, Esam Ibraheem Azhar, Fehmida Bibi, Muhammad Yasir, Aldiouma Diallo, Cheikh Sokhna, Felix Djossou, Véronique Vitton, Catherine Robert, Jean Marc Rolain, Bernard La Scola, Pierre-Edouard Fournier, Anthony Levasseur, Didier Raoult
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引用次数: 0
Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes 应激反应能力的差异决定了李斯特菌种内毒力的异质性和宿主的适应性
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-22 DOI: 10.1038/s41564-024-01859-8
Lukas Hafner, Enzo Gadin, Lei Huang, Arthur Frouin, Fabien Laporte, Charlotte Gaultier, Afonso Vieira, Claire Maudet, Hugo Varet, Alexandra Moura, Hélène Bracq-Dieye, Nathalie Tessaud-Rita, Mylène Maury, Melody Dazas, Rachel Legendre, Pauline Gastineau, Yu-Huan Tsai, Jean-Yves Coppée, Caroline Charlier, Etienne Patin, Rayan Chikhi, Eduardo P. C. Rocha, Alexandre Leclercq, Olivier Disson, Hugues Aschard, Marc Lecuit
Microbial pathogenesis is mediated by the expression of virulence genes. However, as microbes with identical virulence gene content can differ in their pathogenic potential, other virulence determinants must be involved. Here, by combining comparative genomics and transcriptomics of a large collection of isolates of the model pathogen Listeria monocytogenes, time-lapse microscopy, in vitro evolution and in vivo experiments, we show that the individual stress responsiveness of L. monocytogenes isolates determines their respective levels of virulence in vivo and reflects their degree of host adaptation. The transcriptional signature that accounts for the heterogeneity in the virulence of L. monocytogenes species is mediated by the stress response regulator SigB and driven by differential stress responsiveness. The tuning of SigB pathway responsiveness is polygenic and influenced by multiple, individually rare gene variations. This study reveals an overarching determinant of microbial virulence, challenging the paradigm of accessory virulence gene content as the major determinant of intraspecies virulence heterogeneity. Differences in virulence across the Listeria monocytogenes species are determined by the fine-tuning of SigB pathway responsiveness and reflect host adaptation.
微生物致病是由毒力基因的表达介导的。然而,由于毒力基因含量相同的微生物在致病潜能方面可能存在差异,因此必须涉及其他毒力决定因素。在这里,我们通过对大量模式病原体单核细胞增生李斯特菌分离株的比较基因组学和转录组学、延时显微镜、体外进化和体内实验相结合,证明单核细胞增生李斯特菌分离株的个体应激反应性决定了它们各自在体内的毒力水平,并反映了它们对宿主的适应程度。导致单核细胞增多性乳酸杆菌毒力异质性的转录特征由应激反应调节因子 SigB 介导,并由不同的应激反应性驱动。SigB 通路响应性的调整是多基因的,受多种单独罕见基因变异的影响。这项研究揭示了微生物毒力的总体决定因素,挑战了将附属毒力基因含量作为种内毒力异质性主要决定因素的模式。
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引用次数: 0
Parkinson’s drug starves gut microbes of iron 帕金森病药物使肠道微生物缺乏铁元素
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-22 DOI: 10.1038/s41564-024-01863-y
Jan Homolak, Lara Berg, Lisa Maier
Entacapone, a drug used in the treatment of Parkinson’s disease, disrupts gut microbial communities by sequestering iron, creating a competitive advantage for iron-scavenging microbes that often carry antimicrobial resistance and virulence genes.
恩他卡朋是一种用于治疗帕金森病的药物,它能通过封存铁扰乱肠道微生物群落,为通常携带抗菌药耐药性和毒力基因的铁清除微生物创造竞争优势。
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引用次数: 0
The neonatal Fc receptor is a cellular receptor for human astrovirus 新生儿 Fc 受体是人类星状病毒的细胞受体
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-22 DOI: 10.1038/s41564-024-01855-y
Harshad Ingle, Jerome M. Molleston, Paige D. Hall, Duyen Bui, Leran Wang, Karan D. Bhatt, Lynne Foster, Avan Antia, Siyuan Ding, Sanghyun Lee, Daved H. Fremont, Megan T. Baldridge
Human astroviruses (HAstV) are major causes of gastroenteritis, especially in children, and there are no vaccines or antivirals currently available. Little is known about host factors required for their cellular entry. Here we utilized complementary CRISPR-Cas9-based knockout and activation screens to identify neonatal Fc receptor (FcRn) and dipeptidyl-peptidase IV (DPP4) as entry factors for HAstV infection in vitro. Disruption of FcRn or DPP4 reduced HAstV infection in permissive cells and, reciprocally, overexpression of these factors in non-permissive cells was sufficient to promote infection. We observed direct binding of FcRn, but not DPP4, with HAstV virions and the purified spike protein. This suggests that FcRn is a receptor for HAstVs while DPP4 is a cofactor for entry. Inhibitors for DPP4 and FcRn currently in clinical use prevented HAstV infection in cell lines and human enteroids. Our results reveal mechanisms of HAstV entry as well as druggable targets to limit HAstV infection. A CRISPR-based screen identifies neonatal Fc receptor (FcRn) and dipeptidyl-peptidase IV (DPP4) as entry factors for human astrovirus, and targeting them using available therapies effectively prevents infection in human enteroid cultures.
人类星状病毒(HAstV)是导致肠胃炎,尤其是儿童肠胃炎的主要原因,目前还没有疫苗或抗病毒药物。人们对其进入细胞所需的宿主因子知之甚少。在这里,我们利用基于 CRISPR-Cas9 的互补性基因敲除和激活筛选,确定了新生儿 Fc 受体(FcRn)和二肽基肽酶 IV(DPP4)作为体外感染 HAstV 的进入因子。FcRn或DPP4的破坏会减少HAstV在允许细胞中的感染,反之,在非允许细胞中过表达这些因子足以促进感染。我们观察到 FcRn(而非 DPP4)与 HAstV 病毒和纯化的尖峰蛋白直接结合。这表明 FcRn 是 HAstV 的受体,而 DPP4 是进入的辅助因子。目前临床上使用的 DPP4 和 FcRn 抑制剂可阻止 HAstV 在细胞系和人体肠道中的感染。我们的研究结果揭示了 HAstV 的进入机制以及限制 HAstV 感染的药物靶点。
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引用次数: 0
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration 帕金森病药物恩他卡朋通过铁螯合作用破坏肠道微生物群平衡
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-21 DOI: 10.1038/s41564-024-01853-0
Fátima C. Pereira, Xiaowei Ge, Jannie M. Kristensen, Rasmus H. Kirkegaard, Klara Maritsch, Dávid Szamosvári, Stefanie Imminger, David Seki, Juwairiyah B. Shazzad, Yifan Zhu, Marie Decorte, Bela Hausmann, David Berry, Kenneth Wasmund, Arno Schintlmeister, Thomas Böttcher, Ji-Xin Cheng, Michael Wagner
Many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson’s disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance. Entacapone, a Parkinson’s disease medication, sequesters iron resulting in a selective inhibition of gut microbial activity.
许多人类靶向药物会改变肠道微生物组,从而对宿主健康产生影响。然而,这些影响的机制尚不清楚。在这里,我们结合了定量微生物组图谱分析、长读元基因组学、稳定同位素探测和单细胞化学成像技术,研究了两种广泛使用的药物对肠道微生物组的影响。将生理相关浓度的治疗帕金森病的恩他卡朋或治疗精神分裂症的琥珀酸洛沙平与人体粪便样本进行体外培养。这两种药物对微生物活性的影响都很大,比对微生物数量的影响更大。从机理上讲,恩他卡朋能使可用铁元素复杂化并耗尽,从而导致肠道微生物组的组成和功能发生变化。通过补充微生物群可利用铁的水平,可以挽救微生物的生长。此外,恩他卡朋诱导的铁饥饿选择了编码抗微生物抗性和毒力基因的铁清除肠道微生物组成员。这些发现揭示了两种未得到充分研究的药物对整个微生物组的影响,并确定金属螯合是药物诱导微生物组紊乱的一种机制。
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引用次数: 0
Engineering history with Asgard archaea of the kingdom Promethearchaeati 阿斯加德古菌王国普罗米修斯古菌的工程历史
IF 20.5 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-20 DOI: 10.1038/s41564-024-01866-9
Masaru K. Nobu
Multiple histories converge in Masaru Nobu’s story of culturing an archaeon closely related to us eukaryotes.
Masaru Nobu 讲述了培养一种与我们真核生物密切相关的古生物的故事。
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引用次数: 0
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Nature Microbiology
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