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Aerobic adaptation and metabolic dynamics of Propionibacterium freudenreichii DSM 20271: insights from comparative transcriptomics and surfaceome analysis. 弗氏丙酸杆菌(Propionibacterium freudenreichii DSM 20271)的有氧适应和代谢动态:比较转录组学和表面组分析的启示。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 Epub Date: 2024-09-30 DOI: 10.1128/msystems.00615-24
Iida Loivamaa, Annika Sillanpää, Paulina Deptula, Bhawani Chamlagain, Minnamari Edelmann, Petri Auvinen, Tuula A Nyman, Kirsi Savijoki, Vieno Piironen, Pekka Varmanen

Propionibacterium freudenreichii (PFR) DSM 20271T is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271T to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of vitamin B12, pseudovitamin-B12, propionate, and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, tricarboxylic acid cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and α-ketoglutarate availability. Furthermore, in liquid culture, FeSO4 supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding of PFR's physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications.

Importance: The study of the response of Propionibacterium freudenreichii to aerobic growth is crucial for understanding how this bacterium adapts to different environments and produces essential compounds like vitamin B12. By investigating its physiological changes under aerobic conditions, we can gain insights into its metabolic adjustments and potential for enhanced growth. These findings not only deepen our understanding of P. freudenreichii's responses to oxygen availability but also offer valuable information for optimizing its growth in industrial applications. This research sheds light on the adaptive mechanisms of this bacterium, providing a foundation for further exploration and potential applications in various fields.

freudenreichii 丙酸杆菌(PFR)DSM 20271T 是一种以能够在不同环境中生长并产生维生素 B12 而闻名的细菌。尽管它偏好厌氧,但最近的研究阐明了它在有氧条件下的繁殖能力,这促使我们对它在有氧条件下的生理机能进行更深入的探索。在这里,我们采用转录组和表面组的比较分析以及代谢物谱分析,研究了 DSM 20271T 对有氧生长的反应。在受控氧分压(pO2)条件下培养发现,在有氧条件下,生物量的形成显著增加,代谢物的产生也发生了变化,尤其是维生素 B12、假维生素 B12、丙酸盐和乙酸盐。转录组分析发现,参与乳酸代谢、三羧酸循环和电子传递链的基因表达不同,这表明代谢调整适应了有氧环境。此外,表面组分析揭示了表面蛋白质丰度随生长环境而发生的变化,这对适应大气条件具有重要意义。关键化合物的补充实验突出了增强有氧生长的潜力,强调了铁和α-酮戊二酸供应的重要性。此外,在液体培养中,FeSO4 的补充导致血红素生成增加,维生素 B12 生成减少,突出了氧气和铁的可用性对代谢途径的影响。这些发现加深了我们对聚对丙烯酰胺对氧气供应的生理反应的理解,并为优化其在工业应用中的生长提供了启示:研究芽孢杆菌(Propionibacterium freudenreichii)对有氧生长的反应对于了解这种细菌如何适应不同环境并产生维生素 B12 等必需化合物至关重要。通过研究它在有氧条件下的生理变化,我们可以深入了解它的新陈代谢调整和增强生长的潜力。这些发现不仅加深了我们对 P. freudenreichii 对氧气可用性的反应的理解,还为优化其在工业应用中的生长提供了有价值的信息。这项研究揭示了这种细菌的适应机制,为进一步探索和在各个领域的潜在应用奠定了基础。
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引用次数: 0
Genome-centric metagenomics provides insights into the core microbial community and functional profiles of biofloc aquaculture. 以基因组为中心的元基因组学为生物絮团水产养殖的核心微生物群落和功能特征提供了见解。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 Epub Date: 2024-09-24 DOI: 10.1128/msystems.00782-24
Meora Rajeev, Ilsuk Jung, Ilnam Kang, Jang-Cheon Cho
<p><p>Bioflocs are microbial aggregates that play a pivotal role in shaping animal health, gut microbiota, and water quality in biofloc technology (BFT)-based aquaculture systems. Despite the worldwide application of BFT in aquaculture industries, our comprehension of the community composition and functional potential of the floc-associated microbiota (FAB community; ≥3 µm size fractions) remains rudimentary. Here, we utilized genome-centric metagenomic approach to investigate the FAB community in shrimp aquaculture systems, resulting in the reconstruction of 520 metagenome-assembled genomes (MAGs) spanning both bacterial and archaeal domains. Taxonomic analysis identified <i>Pseudomonadota</i> and <i>Bacteroidota</i> as core community members, with approximately 93% of recovered MAGs unclassified at the species level, indicating a large uncharacterized phylogenetic diversity hidden in the FAB community. Functional annotation of these MAGs unveiled their complex carbohydrate-degrading potential and involvement in carbon, nitrogen, and sulfur metabolisms. Specifically, genomic evidence supported ammonium assimilation, autotrophic nitrification, denitrification, dissimilatory nitrate reduction to ammonia, thiosulfate oxidation, and sulfide oxidation pathways, suggesting the FAB community's versatility for both aerobic and anaerobic metabolisms. Conversely, genes associated with heterotrophic nitrification, anaerobic ammonium oxidation, assimilatory nitrate reduction, and sulfate reduction were undetected. Members of <i>Rhodobacteraceae</i> emerged as the most abundant and metabolically versatile taxa in this intriguing community. Our MAGs compendium is expected to expand the available genome collection from such underexplored aquaculture environments. By elucidating the microbial community structure and metabolic capabilities, this study provides valuable insights into the key biogeochemical processes occurring in biofloc aquacultures and the major microbial contributors driving these processes.</p><p><strong>Importance: </strong>Biofloc technology has emerged as a sustainable aquaculture approach, utilizing microbial aggregates (bioflocs) to improve water quality and animal health. However, the specific microbial taxa within this intriguing community responsible for these benefits are largely unknown. Compounding this challenge, many bacterial taxa resist laboratory cultivation, hindering taxonomic and genomic analyses. To address these gaps, we employed metagenomic binning approach to recover over 500 microbial genomes from floc-associated microbiota of biofloc aquaculture systems operating in South Korea and China. Through taxonomic and genomic analyses, we deciphered the functional gene content of diverse microbial taxa, shedding light on their potential roles in key biogeochemical processes like nitrogen and sulfur metabolisms. Notably, our findings underscore the taxa-specific contributions of microbes in aquaculture environments, particularl
生物絮团是一种微生物聚集体,在基于生物絮团技术(BFT)的水产养殖系统中对动物健康、肠道微生物群和水质的形成起着关键作用。尽管生物絮团技术在水产养殖业中的应用遍及全球,但我们对絮团相关微生物群(FAB 群,≥3 µm 大小的部分)的群落组成和功能潜力的了解仍然很有限。在这里,我们利用以基因组为中心的元基因组学方法研究了对虾养殖系统中的絮凝物群落,重建了 520 个元基因组组装基因组(MAGs),涵盖了细菌和古细菌两个领域。分类学分析确定假单胞菌和类杆菌为群落的核心成员,约 93% 的已恢复 MAGs 在物种水平上未分类,这表明在 FAB 群落中隐藏着大量未定性的系统发育多样性。对这些 MAGs 的功能注释揭示了它们复杂的碳水化合物降解潜力,以及参与碳、氮和硫代谢的情况。具体来说,基因组证据支持氨同化、自养硝化、反硝化、硝酸盐异纤还原成氨、硫代硫酸盐氧化和硫化物氧化途径,这表明 FAB 群落在好氧和厌氧代谢方面具有多功能性。相反,与异养硝化、厌氧铵氧化、同化作用硝酸盐还原和硫酸盐还原相关的基因却未被检测到。在这一引人入胜的群落中,罗杆菌科成员是数量最多、代谢能力最强的类群。我们的 MAGs 汇编有望扩大此类未充分开发的水产养殖环境中的可用基因组收集。通过阐明微生物群落结构和代谢能力,本研究为了解生物絮团水产养殖中发生的关键生物地球化学过程以及驱动这些过程的主要微生物贡献者提供了宝贵的见解:生物絮团技术已成为一种可持续的水产养殖方法,它利用微生物聚集体(生物絮团)来改善水质和动物健康。然而,在这一引人入胜的群落中,产生这些益处的具体微生物类群却大多不为人知。此外,许多细菌类群对实验室培养有抵触情绪,阻碍了分类学和基因组学分析。为了填补这些空白,我们采用了元基因组分选方法,从韩国和中国生物絮团水产养殖系统的絮团相关微生物群中恢复了 500 多个微生物基因组。通过分类和基因组分析,我们破译了不同微生物类群的功能基因含量,揭示了它们在氮和硫代谢等关键生物地球化学过程中的潜在作用。值得注意的是,我们的研究结果强调了水产养殖环境中微生物类群的特定贡献,尤其是在复杂的碳降解和去除氨、硝酸盐和硫化物等有毒物质方面。
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引用次数: 0
Metapopulation model of phage therapy of an acute Pseudomonas aeruginosa lung infection. 噬菌体治疗急性铜绿假单胞菌肺部感染的群体模型。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 Epub Date: 2024-09-04 DOI: 10.1128/msystems.00171-24
Rogelio A Rodriguez-Gonzalez, Quentin Balacheff, Laurent Debarbieux, Jacopo Marchi, Joshua S Weitz
<p><p>Infections caused by multidrug resistant (MDR) pathogenic bacteria are a global health threat. Bacteriophages ("phage") are increasingly used as alternative or last-resort therapeutics to treat patients infected by MDR bacteria. However, the therapeutic outcomes of phage therapy may be limited by the emergence of phage resistance during treatment and/or by physical constraints that impede phage-bacteria interactions <i>in vivo</i>. In this work, we evaluate the role of lung spatial structure on the efficacy of phage therapy for <i>Pseudomonas aeruginosa</i> infections. To do so, we developed a spatially structured metapopulation network model based on the geometry of the bronchial tree, including host innate immune responses and the emergence of phage-resistant bacterial mutants. We model the ecological interactions between bacteria, phage, and the host innate immune system at the airway (node) level. The model predicts the synergistic elimination of a <i>P. aeruginosa</i> infection due to the combined effects of phage and neutrophils, given the sufficient innate immune activity and efficient phage-induced lysis. The metapopulation model simulations also predict that MDR bacteria are cleared faster at distal nodes of the bronchial tree. Notably, image analysis of lung tissue time series from wild-type and lymphocyte-depleted mice revealed a concordant, statistically significant pattern: infection intensity cleared in the bottom before the top of the lungs. Overall, the combined use of simulations and image analysis of <i>in vivo</i> experiments further supports the use of phage therapy for treating acute lung infections caused by <i>P. aeruginosa,</i> while highlighting potential limits to therapy in a spatially structured environment given impaired innate immune responses and/or inefficient phage-induced lysis.</p><p><strong>Importance: </strong>Phage therapy is increasingly employed as a compassionate treatment for severe infections caused by multidrug-resistant (MDR) bacteria. However, the mixed outcomes observed in larger clinical studies highlight a gap in understanding when phage therapy succeeds or fails. Previous research from our team, using <i>in vivo</i> experiments and single-compartment mathematical models, demonstrated the synergistic clearance of acute <i>P. aeruginosa</i> pneumonia by phage and neutrophils despite the emergence of phage-resistant bacteria. In fact, the lung environment is highly structured, prompting the question of whether immunophage synergy explains the curative treatment of <i>P. aeruginosa</i> when incorporating realistic physical connectivity. To address this, we developed a metapopulation network model mimicking the lung branching structure to assess phage therapy efficacy for MDR <i>P. aeruginosa</i> pneumonia. The model predicts the synergistic elimination of <i>P. aeruginosa</i> by phage and neutrophils but emphasizes potential challenges in spatially structured environments, suggesting that higher
耐多药(MDR)病原菌引起的感染是一个全球性的健康威胁。噬菌体("噬菌体")越来越多地被用作治疗多重耐药细菌感染患者的替代疗法或最后手段。然而,噬菌体疗法的治疗效果可能会受到治疗过程中出现的噬菌体抗药性和/或阻碍体内噬菌体与细菌相互作用的物理限制。在这项研究中,我们评估了肺部空间结构对噬菌体疗法治疗铜绿假单胞菌感染疗效的影响。为此,我们根据支气管树的几何形状开发了一个空间结构元种群网络模型,包括宿主先天性免疫反应和噬菌体抗性细菌突变体的出现。我们模拟了细菌、噬菌体和宿主先天免疫系统在气道(节点)层面上的生态相互作用。该模型预测,在先天性免疫活性充足和噬菌体诱导的高效裂解作用下,噬菌体和中性粒细胞的联合作用将协同消除铜绿假单胞菌感染。元群体模型模拟还预测,MDR 细菌在支气管树远端结节的清除速度更快。值得注意的是,对野生型小鼠和淋巴细胞耗竭型小鼠肺组织时间序列的图像分析显示了一种一致的、具有统计学意义的模式:肺底部的感染强度先于肺顶部的感染强度被清除。总之,结合使用模拟和体内实验图像分析,进一步支持了使用噬菌体疗法治疗铜绿假单胞菌引起的急性肺部感染,同时强调了在先天免疫反应受损和/或噬菌体诱导的裂解效率低下的空间结构环境中治疗的潜在局限性:噬菌体疗法越来越多地被用作治疗耐多药(MDR)细菌引起的严重感染的同情疗法。然而,在大型临床研究中观察到的结果喜忧参半,这凸显出在了解噬菌体疗法的成败方面存在差距。我们团队之前的研究利用体内实验和单室数学模型证明,尽管出现了噬菌体耐药菌,但噬菌体和中性粒细胞能协同清除急性铜绿假单胞菌肺炎。事实上,肺部环境是高度结构化的,这就提出了一个问题:在结合现实物理连接性的情况下,免疫噬菌体的协同作用能否解释铜绿假单胞菌肺炎的治疗效果?为了解决这个问题,我们开发了一个模仿肺部分支结构的元群体网络模型,以评估噬菌体疗法对 MDR 铜绿假单胞菌肺炎的疗效。该模型预测了噬菌体和中性粒细胞对铜绿假单胞菌的协同清除作用,但强调了空间结构环境中的潜在挑战,表明要成功清除细菌可能需要更高的先天免疫水平。模型模拟揭示了病原体清除的空间模式,即支气管树远端结节的铜绿假单胞菌清除速度快于初级结节。有趣的是,对受感染小鼠的图像分析表明了一种一致且具有统计学意义的模式:感染强度在肺底部先于顶部清除。建模和图像分析的结合使用支持了噬菌体疗法在急性铜绿假单胞菌肺炎中的应用,同时也强调了在空间结构的体内环境中治疗成功所面临的潜在挑战,包括先天性免疫反应受损和噬菌体疗效降低。
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引用次数: 0
Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome. 有针对性地发现肠道微生物组重塑化合物,用于治疗全身炎症反应综合征。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 Epub Date: 2024-09-05 DOI: 10.1128/msystems.00788-24
Luyao Liu, Lin Ma, Huan Liu, Fan Zhao, Pu Li, Junhua Zhang, Xin Lü, Xin Zhao, Yanglei Yi

Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death. Modulating the gut microbiome is a promising therapeutic approach for managing SIRS. This study assesses the therapeutic potential of the Xuanfei Baidu (XFBD) formula in treating SIRS. The results showed that XFBD administration effectively reduced mortality rates and inflammation in SIRS mice. Using 16S rRNA sequencing and fecal microbiota transplantation (FMT), we substantiated that the therapeutic effects of XFBD are partly attributed to gut microbiota modulation. We conducted in vitro experiments to accurately assess the gut microbiome remodeling effects of 51 compounds isolated from XFBD. These compounds exhibited varying abilities to induce a microbial structure that closely resembles that of the healthy control group. By quantifying their impact on microbial structure and clustering their regulatory patterns, we devised multiple gut microbiome remodeling compound (GMRC) cocktails. GMRC cocktail C, comprising aucubin, gentiopicroside, syringic acid, gallic acid, p-hydroxybenzaldehyde, para-hydroxybenzoic acid, and isoimperatorin, demonstrated superior efficacy in treating SIRS compared to a single compound or to other cocktails. Finally, in vitro experiments showcased that GMRC cocktail C effectively rebalanced bacteria composition in SIRS patients. This study underscores XFBD's therapeutic potential in SIRS and highlights the importance of innovative treatment approaches for this disease by targeting the gut microbiota.IMPORTANCEDeveloping effective treatment strategies for systemic inflammatory response syndrome (SIRS) is crucial due to its severe and often life-threatening nature. While traditional treatments like dexamethasone have shown efficacy, they also come with significant side effects and limitations. This study makes significant strides by demonstrating that the Xuanfei Baidu (XFBD) formula can substantially reduce mortality rates and inflammation in SIRS mice through effective modulation of the gut microbiota. By quantitatively assessing the impact of 51 compounds derived from XFBD on the gut microbiome, we developed a potent gut microbiome remodeling compound cocktail. This cocktail outperformed individual compounds and other mixtures in efficacy against SIRS. These findings highlight the potential of XFBD as a therapeutic solution for SIRS and underscore the critical role of innovative strategies targeting the gut microbiota in addressing this severe inflammatory condition.

全身炎症反应综合征(SIRS)是一种严重的炎症反应,可导致器官功能障碍和死亡。调节肠道微生物组是控制 SIRS 的一种很有前景的治疗方法。本研究评估了玄参方治疗 SIRS 的潜力。结果显示,服用玄参白术散能有效降低SIRS小鼠的死亡率和炎症反应。通过 16S rRNA 测序和粪便微生物群移植(FMT),我们证实了 XFBD 的治疗效果部分归功于肠道微生物群的调节。我们进行了体外实验,以准确评估从 XFBD 中分离出的 51 种化合物对肠道微生物群重塑的影响。这些化合物在诱导与健康对照组非常相似的微生物结构方面表现出不同的能力。通过量化这些化合物对微生物结构的影响并对其调控模式进行聚类,我们设计出了多种肠道微生物组重塑化合物(GMRC)鸡尾酒。由杜仲甙、龙胆甙、丁香酸、没食子酸、对羟基苯甲醛、对羟基苯甲酸和异橙皮甙组成的 GMRC 鸡尾酒 C 在治疗 SIRS 方面的疗效优于单一化合物或其他鸡尾酒。最后,体外实验表明,GMRC 鸡尾酒 C 能有效地重新平衡 SIRS 患者体内的细菌组成。这项研究强调了 XFBD 在 SIRS 中的治疗潜力,并突出了通过靶向肠道微生物群来创新治疗这种疾病的方法的重要性。重要意义由于全身炎症反应综合征(SIRS)病情严重且常常危及生命,因此开发有效的治疗策略至关重要。虽然地塞米松等传统疗法已显示出疗效,但它们也有很大的副作用和局限性。这项研究取得了重大进展,证明了宣飞百度(XFBD)配方可以通过有效调节肠道微生物群来大幅降低 SIRS 小鼠的死亡率和炎症反应。通过定量评估从玄参中提取的 51 种化合物对肠道微生物群的影响,我们开发出了一种强效的肠道微生物群重塑复合鸡尾酒。这种鸡尾酒对 SIRS 的疗效优于单个化合物和其他混合物。这些发现凸显了 XFBD 作为 SIRS 治疗方案的潜力,并强调了针对肠道微生物群的创新策略在解决这一严重炎症问题中的关键作用。
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引用次数: 0
MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes. MVP:模块化病毒组学管道,用于从元基因组中识别、过滤、聚类、注释和分选病毒。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-22 Epub Date: 2024-10-01 DOI: 10.1128/msystems.00888-24
Clément Coclet, Antonio Pedro Camargo, Simon Roux

While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.

虽然有许多计算框架和工作流程可用于从元基因组数据中恢复原核生物和真核生物基因组,但专门为病毒组学分析设计的管道数量有限。仅在过去几年中就开发出了许多病毒组学工具,但对于生物信息学经验有限的科学家来说,要利用最先进的方法和标准轻松地恢复病毒基因组、评估质量、注释基因、去除复制、分配分类以及计算相对丰度和覆盖率是一项挑战。在这里,我们介绍模块化病毒组学管道(MVP)v.1.0,这是一个用 Python 编写的用户友好型管道,提供了一个执行标准病毒组学分析的简单框架。MVP 结合了多种工具,可实现病毒基因组鉴定、基因组质量鉴定、过滤、聚类、分类和功能注释、基因组分选以及可用于下游生态分析的结果综合汇总。总之,MVP 提供了一个标准化和可重复的管道,可从大规模测序数据(包括元基因组、元转录组、病毒组和分离基因组)中对病毒进行广泛和稳健的表征。作为一个典型的使用案例,我们展示了如何将整个 MVP 管道应用于一组来自湿地沉积物的 20 个元基因组,只需通过命令行执行 10 个模块,就能鉴定出 11,656 个病毒等位基因和 8,145 个病毒操作分类单元(vOTU),显示出明显的贝塔多样性模式。此外,作为一个动态包装器,MVP 的设计目的是不断纳入更新和集成新工具,确保其在快速发展的病毒组学领域中的持续相关性。MVP 可在 https://gitlab.com/ccoclet/mvp 网站上查阅,也可作为版本化软件包在 PyPi 和 Conda 中使用。重要意义我们工作的意义在于开发了模块化病毒组学管道(MVP),这是一个专为病毒组学分析定制的集成式用户友好管道。MVP 的突出之处在于其模块化设计,可确保轻松安装、执行和集成新工具和数据库。MVP 结合了 geNomad 和 CheckV 等最先进的工具,可提供高质量的病毒基因组恢复、分类和宿主分配以及功能注释,解决了现有管道的局限性。MVP 能够处理各种类型的样本,包括环境样本、人类微生物组样本和植物相关样本,使其成为微生物组研究领域的多功能工具。通过标准化分析流程和提供易于解释的结果,MVP 使研究人员能够对病毒群落进行全面研究,极大地推动了我们对病毒生态学及其对各种生态系统影响的了解。
{"title":"MVP: a modular viromics pipeline to identify, filter, cluster, annotate, and bin viruses from metagenomes.","authors":"Clément Coclet, Antonio Pedro Camargo, Simon Roux","doi":"10.1128/msystems.00888-24","DOIUrl":"10.1128/msystems.00888-24","url":null,"abstract":"<p><p>While numerous computational frameworks and workflows are available for recovering prokaryote and eukaryote genomes from metagenome data, only a limited number of pipelines are designed specifically for viromics analysis. With many viromics tools developed in the last few years alone, it can be challenging for scientists with limited bioinformatics experience to easily recover, evaluate quality, annotate genes, dereplicate, assign taxonomy, and calculate relative abundance and coverage of viral genomes using state-of-the-art methods and standards. Here, we describe Modular Viromics Pipeline (MVP) v.1.0, a user-friendly pipeline written in Python and providing a simple framework to perform standard viromics analyses. MVP combines multiple tools to enable viral genome identification, characterization of genome quality, filtering, clustering, taxonomic and functional annotation, genome binning, and comprehensive summaries of results that can be used for downstream ecological analyses. Overall, MVP provides a standardized and reproducible pipeline for both extensive and robust characterization of viruses from large-scale sequencing data including metagenomes, metatranscriptomes, viromes, and isolate genomes. As a typical use case, we show how the entire MVP pipeline can be applied to a set of 20 metagenomes from wetland sediments using only 10 modules executed via command lines, leading to the identification of 11,656 viral contigs and 8,145 viral operational taxonomic units (vOTUs) displaying a clear beta-diversity pattern. Further, acting as a dynamic wrapper, MVP is designed to continuously incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field of viromics. MVP is available at https://gitlab.com/ccoclet/mvp and as versioned packages in PyPi and Conda.IMPORTANCEThe significance of our work lies in the development of Modular Viromics Pipeline (MVP), an integrated and user-friendly pipeline tailored exclusively for viromics analyses. MVP stands out due to its modular design, which ensures easy installation, execution, and integration of new tools and databases. By combining state-of-the-art tools such as geNomad and CheckV, MVP provides high-quality viral genome recovery and taxonomy and host assignment, and functional annotation, addressing the limitations of existing pipelines. MVP's ability to handle diverse sample types, including environmental, human microbiome, and plant-associated samples, makes it a versatile tool for the broader microbiome research community. By standardizing the analysis process and providing easily interpretable results, MVP enables researchers to perform comprehensive studies of viral communities, significantly advancing our understanding of viral ecology and its impact on various ecosystems.</p>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-10-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11498083/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142350275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
The choice of 16S rRNA gene sequence analysis impacted characterization of highly variable surface microbiota in dairy processing environments. 16S rRNA 基因序列分析的选择影响了乳制品加工环境中高度多变的表面微生物群的特征描述。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-21 DOI: 10.1128/msystems.00620-24
Sarah E Daly, Jingzhang Feng, Devin Daeschel, Jasna Kovac, Abigail B Snyder

Accurate knowledge of the microbiota collected from surfaces in food processing environments is important for food quality and safety. This study assessed discrepancies in taxonomic composition and alpha and beta diversity values generated from eight different bioinformatic workflows for the analysis of 16S rRNA gene sequences extracted from the microbiota collected from surfaces in dairy processing environments. We found that the microbiota collected from environmental surfaces varied widely in density (0-9.09 log10 CFU/cm2) and Shannon alpha diversity (0.01-3.40). Consequently, depending on the sequence analysis method used, characterization of low-abundance genera (i.e., below 1% relative abundance) and the number of genera identified (114-173 genera) varied considerably. Some low-abundance genera, including Listeria, varied between the amplicon sequence variant (ASV) and operational taxonomic unit (OTU) methods. Centered log-ratio transformation inflated alpha and beta diversity values compared to rarefaction. Furthermore, the ASV method also inflated alpha and beta diversity values compared to the OTU method (P < 0.05). Therefore, for sparse, uneven, low-density data sets, the OTU method and rarefaction are better for taxonomic and ecological characterization of surface microbiota.IMPORTANCECulture-dependent environmental monitoring programs are used by the food industry to identify foodborne pathogens and spoilage biota on surfaces in food processing environments. The use of culture-independent 16S rRNA amplicon sequencing to characterize this surface microbiota has been proposed as a tool to enhance environmental monitoring. However, there is no consensus on the most suitable bioinformatic analyses to accurately capture the diverse levels and types of bacteria on surfaces in food processing environments. Here, we quantify the impact of different bioinformatic analyses on the results and interpretation of 16S rRNA amplicon sequences collected from three cultured dairy facilities in New York State. This study provides guidance for the selection of appropriate 16S rRNA analysis procedures for studying environmental microbiota in dairy processing environments.

准确了解从食品加工环境表面收集的微生物群对食品质量和安全非常重要。本研究评估了从乳制品加工环境表面采集的微生物群中提取的 16S rRNA 基因序列分析的八个不同生物信息学工作流程所产生的分类组成、α 和β多样性值的差异。我们发现,从环境表面采集的微生物群在密度(0-9.09 log10 CFU/cm2)和香农α多样性(0.01-3.40)方面差异很大。因此,根据所使用的序列分析方法,低丰度菌属(即相对丰度低于 1%)的特征和已鉴定菌属的数量(114-173 个)差异很大。包括李斯特菌在内的一些低丰度属在扩增子序列变异法(ASV)和操作分类单元法(OTU)之间存在差异。与稀释法相比,以对数比率为中心的转换使α和β多样性值增大。此外,与 OTU 方法相比,ASV 方法也提高了阿尔法和贝塔多样性值(P < 0.05)。因此,对于稀疏、不均匀、低密度的数据集,OTU 法和稀释法更适合表面微生物群的分类和生态特征描述。有人建议使用与培养无关的 16S rRNA 扩增子测序来描述这种表面微生物群,作为加强环境监测的一种工具。然而,对于最合适的生物信息学分析方法还没有达成共识,无法准确捕捉食品加工环境中表面细菌的不同水平和类型。在此,我们量化了不同生物信息学分析对从纽约州三家培养乳制品厂采集的 16S rRNA 扩增子序列的结果和解释的影响。这项研究为研究乳制品加工环境中的环境微生物群选择合适的 16S rRNA 分析程序提供了指导。
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引用次数: 0
Integrated analysis of metabolome and microbiome in a rat model of perimenopausal syndrome. 围绝经期综合征大鼠模型中代谢组和微生物组的综合分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-21 DOI: 10.1128/msystems.00623-24
Yanqiu Wei, Juanjuan Shi, Jianhua Wang, Zongyan Hu, Min Wang, Wen Wang, Xiujuan Cui

The objectives of this study are to examine the disparities in serum and intestinal tissue metabolites between a perimenopausal rat model and control rats and to analyze the diversity and functionality of intestinal microorganisms to determine the potential correlation between intestinal flora and metabolites. We established a rat model of perimenopausal syndrome (PMS) and performed an integrated analysis of metabolome and microbiome. Orthogonal partial least-squares discriminant analysis scores and replacement tests indicated distinct separations of anion and cation levels between serum and intestinal samples of the model and control groups. Furthermore, lipids and lipid-like molecules constituted the largest percentage of HMDB compounds in both serum and intestinal tissues, followed by organic acids and derivatives, and organoheterocyclic compounds, with other compounds showing significant variability. Moreover, analysis of diversity and functional enrichment of the intestinal microflora and correlation analysis with metabolites revealed significant variability in the composition of the intestinal flora between the normal control and perimenopausal groups, with these differentially expressed intestinal flora strongly correlated with their metabolites. The findings of this study are expected to contribute to understanding the indications and contraindications for estrogen application in perimenopausal women and to aid in the development of appropriate therapeutic agents.

Importance: In this work, we employed 16S ribosomal RNA gene sequencing to analyze the gut microbes in stool samples. In addition, we conducted an ultra-high-performance liquid chromatography-tandem mass spectrometry-based metabolomics approach on gut tissue and serum obtained from rats with perimenopausal syndrome (PMS) and healthy controls. By characterizing the composition and metabolomic properties of gut microbes in PMS rats, we aim to enhance our understanding of their role in women's health, emphasizing the significance of regulating gut microbes in the context of menopausal women's well-being. We aim to provide a theoretical basis for the prevention and treatment of PMS in terms of gut microflora as well as metabolism.

本研究的目的是检测围绝经期大鼠模型与对照组大鼠之间血清和肠道组织代谢物的差异,并分析肠道微生物的多样性和功能性,以确定肠道菌群与代谢物之间的潜在相关性。我们建立了围绝经期综合征(PMS)大鼠模型,并对代谢组和微生物组进行了综合分析。正交偏最小二乘判别分析得分和置换检验表明,模型组和对照组的血清和肠道样本中阴离子和阳离子水平有明显的分离。此外,在血清和肠道组织中,脂质和类脂质分子在 HMDB 化合物中所占的比例最大,其次是有机酸及其衍生物和有机杂环化合物,其他化合物则表现出显著的差异性。此外,肠道微生物菌群的多样性和功能富集分析以及与代谢物的相关性分析表明,正常对照组和围绝经期组的肠道菌群组成存在显著差异,这些差异表达的肠道菌群与其代谢物密切相关。本研究的结果有望帮助了解围绝经期妇女应用雌激素的适应症和禁忌症,并有助于开发适当的治疗药物:在这项工作中,我们采用 16S 核糖体 RNA 基因测序分析了粪便样本中的肠道微生物。此外,我们还对围绝经期综合征(PMS)大鼠和健康对照组大鼠的肠道组织和血清进行了基于超高效液相色谱-串联质谱的代谢组学研究。通过分析围绝经期综合征大鼠肠道微生物的组成和代谢组学特性,我们希望加深对它们在女性健康中所起作用的了解,强调调节肠道微生物对更年期女性健康的重要意义。我们的目标是从肠道微生物区系和新陈代谢方面为经前综合征的预防和治疗提供理论依据。
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引用次数: 0
Correction for Kwan et al., "Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes". 更正 Kwan 等人,"墨西哥裔美国人的肠道噬菌体:代谢功能障碍相关性脂肪肝和糖尿病的高危人群"。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-18 DOI: 10.1128/msystems.01297-24
Suet-Ying Kwan, Caroline M Sabotta, Lorenzo R Cruz, Matthew C Wong, Nadim J Ajami, Joseph B McCormick, Susan P Fisher-Hoch, Laura Beretta
{"title":"Correction for Kwan et al., \"Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes\".","authors":"Suet-Ying Kwan, Caroline M Sabotta, Lorenzo R Cruz, Matthew C Wong, Nadim J Ajami, Joseph B McCormick, Susan P Fisher-Hoch, Laura Beretta","doi":"10.1128/msystems.01297-24","DOIUrl":"https://doi.org/10.1128/msystems.01297-24","url":null,"abstract":"","PeriodicalId":18819,"journal":{"name":"mSystems","volume":null,"pages":null},"PeriodicalIF":5.0,"publicationDate":"2024-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142470275","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
E.PathDash, pathway activation analysis of publicly available pathogen gene expression data. E.PathDash,对公开病原体基因表达数据进行通路激活分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-18 DOI: 10.1128/msystems.01030-24
Lily Taub, Thomas H Hampton, Sharanya Sarkar, Georgia Doing, Samuel L Neff, Carson E Finger, Kiyoshi Ferreira Fukutani, Bruce A Stanton

E.PathDash facilitates re-analysis of gene expression data from pathogens clinically relevant to chronic respiratory diseases, including a total of 48 studies, 548 samples, and 404 unique treatment comparisons. The application enables users to assess broad biological stress responses at the KEGG pathway or gene ontology level and also provides data for individual genes. E.PathDash reduces the time required to gain access to data from multiple hours per data set to seconds. Users can download high-quality images such as volcano plots and boxplots, differential gene expression results, and raw count data, making it fully interoperable with other tools. Importantly, users can rapidly toggle between experimental comparisons and different studies of the same phenomenon, enabling them to judge the extent to which observed responses are reproducible. As a proof of principle, we invited two cystic fibrosis scientists to use the application to explore scientific questions relevant to their specific research areas. Reassuringly, pathway activation analysis recapitulated results reported in original publications, but it also yielded new insights into pathogen responses to changes in their environments, validating the utility of the application. All software and data are freely accessible, and the application is available at scangeo.dartmouth.edu/EPathDash.

Importance: Chronic respiratory illnesses impose a high disease burden on our communities and people with respiratory diseases are susceptible to robust bacterial infections from pathogens, including Pseudomonas aeruginosa and Staphylococcus aureus, that contribute to morbidity and mortality. Public gene expression datasets generated from these and other pathogens are abundantly available and an important resource for synthesizing existing pathogenic research, leading to interventions that improve patient outcomes. However, it can take many hours or weeks to render publicly available datasets usable; significant time and skills are needed to clean, standardize, and apply reproducible and robust bioinformatic pipelines to the data. Through collaboration with two microbiologists, we have shown that E.PathDash addresses this problem, enabling them to elucidate pathogen responses to a variety of over 400 experimental conditions and generate mechanistic hypotheses for cell-level behavior in response to disease-relevant exposures, all in a fraction of the time.

E.PathDash 可帮助重新分析与慢性呼吸道疾病临床相关的病原体的基因表达数据,包括总共 48 项研究、548 个样本和 404 个独特的治疗比较。该应用程序使用户能够在 KEGG 通路或基因本体水平上评估广泛的生物应激反应,还能提供单个基因的数据。E.PathDash 可将访问数据所需的时间从每个数据集数小时缩短到数秒。用户可以下载火山图和箱形图等高质量图像、差异基因表达结果和原始计数数据,使其与其他工具完全互操作。重要的是,用户可以在实验比较和同一现象的不同研究之间快速切换,从而判断观察到的反应在多大程度上具有可重复性。作为原理验证,我们邀请了两位囊性纤维化科学家使用该应用程序来探索与其特定研究领域相关的科学问题。令人欣慰的是,通路激活分析再现了原始出版物中报告的结果,而且还对病原体对其环境变化的反应提出了新的见解,从而验证了该应用程序的实用性。所有软件和数据均可免费获取,应用程序可在 scangeo.dartmouth.edu/EPathDash.Importance 上查阅:慢性呼吸道疾病给我们的社区带来了沉重的疾病负担,呼吸道疾病患者很容易受到包括铜绿假单胞菌和金黄色葡萄球菌在内的病原体的细菌感染,从而导致发病和死亡。从这些病原体和其他病原体生成的公共基因表达数据集非常丰富,是综合现有病原体研究的重要资源,可用于改善患者预后的干预措施。然而,要使公开的数据集可用,可能需要数小时或数周的时间;需要大量的时间和技能对数据进行清理、标准化,并应用可重复的、强大的生物信息学管道。通过与两位微生物学家的合作,我们已经证明 E.PathDash 能够解决这个问题,使他们能够在极短的时间内阐明病原体对 400 多种实验条件的反应,并生成细胞级行为对疾病相关暴露的机理假设。
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引用次数: 0
Integrated analysis of microbiota and gut microbial metabolites in blood for breast cancer. 乳腺癌血液中微生物群和肠道微生物代谢物的综合分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-18 DOI: 10.1128/msystems.00643-24
Yu Peng, Jiale Gu, Fubin Liu, Peng Wang, Xixuan Wang, Changyu Si, Jianxiao Gong, Huijun Zhou, Ailing Qin, Fangfang Song

Gut microbiota and associated metabolites have been linked to breast carcinogenesis. Evidences demonstrate blood microbiota primarily originates from the gut and may act as a biomarker for breast cancer. We aimed to characterize the microbiota-gut microbial metabolites cross-talk in blood and develop a composite diagnostic panel for breast cancer. We performed 16S rRNA gene sequencing and metabolomics profiling on blood samples from 107 breast cancer cases and 107 age-paired controls. We found that the alpha diversity of the blood microbiota was decreased in breast cancer compared to controls. There were significantly different profiles of microbiota and gut microbial metabolites in blood between these two groups, with nine bacterial genera and four gut microbial metabolites increased in patients, while thirty-nine bacterial genera and two gut microbial metabolites increased in controls. Some breast cancer-associated gut microbial metabolites were linked to differential blood microbiota, and a composite microbiota-metabolite diagnostic panel was further developed with an area under the curve of 0.963 for breast cancer. This study underscored the pivotal role of microbiota and gut microbial metabolites in blood and their interactions for breast carcinogenesis, as well as the potential of a composite diagnostic panel as a non-invasive biomarker for breast cancer.IMPORTANCEOur integrated analysis demonstrated altered profiles of microbiota and gut microbial metabolites in blood for breast cancer patients. The extensive correlation between microbiota and gut microbial metabolites in blood assisted the understanding of the pathogenesis of breast cancer. The good performance of a composite microbiota-gut microbial metabolites panel in blood suggested a non-invasive approach for breast cancer detection and a novel strategy for better diagnosis and prevention of breast cancer in the future.

肠道微生物群和相关代谢物与乳腺癌的发生有关。有证据表明,血液微生物群主要来自肠道,可作为乳腺癌的生物标志物。我们的目的是描述血液中微生物群-肠道微生物代谢物交叉作用的特征,并开发一个乳腺癌综合诊断面板。我们对 107 例乳腺癌病例和 107 例年龄配对对照的血液样本进行了 16S rRNA 基因测序和代谢组学分析。我们发现,与对照组相比,乳腺癌患者血液微生物群的α多样性降低了。这两组患者血液中的微生物群和肠道微生物代谢物有明显差异,患者血液中的九个细菌属和四个肠道微生物代谢物增加,而对照组血液中的三十九个细菌属和两个肠道微生物代谢物增加。一些与乳腺癌相关的肠道微生物代谢物与不同的血液微生物群相关联,并进一步开发了一个复合微生物群-代谢物诊断面板,对乳腺癌的曲线下面积为 0.963。这项研究强调了血液中的微生物群和肠道微生物代谢物及其相互作用对乳腺癌发生的关键作用,以及复合诊断面板作为乳腺癌非侵入性生物标志物的潜力。血液中微生物群和肠道微生物代谢物之间的广泛相关性有助于了解乳腺癌的发病机制。血液中微生物群-肠道微生物代谢物复合面板的良好性能表明,这是一种非侵入性的乳腺癌检测方法,也是未来更好地诊断和预防乳腺癌的一种新策略。
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