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Association of intratumoral microbiome diversity with hepatocellular carcinoma prognosis. 肿瘤内微生物群多样性与肝癌预后的关系。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-11 DOI: 10.1128/msystems.00765-24
Fengle Jiang, Yuan Dang, Zheting Zhang, Yanan Yan, Yingchao Wang, Yi Chen, Lihong Chen, Jialiang Zhang, Jingfeng Liu, Jianmin Wang

The evidence that intratumoral microbiomes, as a rising hallmark of cancer, have a profound impact on cancer phenotypes is increasingly compelling. However, the impact of the composition and diversity of the intratumoral microbiome on the prognosis of patients undergoing surgical resection for hepatocellular carcinoma (HCC) remains incompletely understood. In this study, we revealed a high abundance of bacteria in the neoplastic tissues. The presence of bacterial lipopolysaccharide and lipoteichoic acid was detected alongside tumor-associated immune cells. By utilizing 16S rRNA gene sequencing, we identified a specific intratumoral microbiome signature that was highly predictive of the prognosis for HCC patients who underwent surgical resection. Specifically, the presence of Intestinimonas, Brachybacterium, and Rothia were identified as independent risk factors for the overall survival of HCC patients who underwent surgical resection.IMPORTANCEAlthough some studies have shown an abundance of bacteria in hepatocellular carcinoma (HCC), there is still limited understanding of the composition and diversity of the intratumoral microbiome that is favorable or adverse to the prognosis of HCC patients. Our results indicated that a greater abundance of bacteria could be observed in the neoplastic tissues than in nonneoplastic tissues. Bacterial cell wall components largely coincided with tumor-associated immune cells. The bacteria in the long overall survival (LOS) group were associated with metabolism and cytokine‒cytokine receptor interaction pathways, while bacteria in the short overall survival (SOS) group were associated with proinflammatory and cell proliferation pathways. Notably, specific taxa could independently predict HCC prognosis. Based on these findings, intratumoral microbiomes facilitate the use of precision medicine in clinical practice.

越来越多的证据表明,肿瘤内微生物组作为癌症的一个日益上升的标志,对癌症表型具有深远的影响。然而,肿瘤内微生物组的组成和多样性对肝细胞癌(HCC)手术切除患者预后的影响尚不完全清楚。在这项研究中,我们发现肿瘤组织中有大量的细菌。在肿瘤相关免疫细胞旁检测到细菌脂多糖和脂壁酸的存在。通过使用16S rRNA基因测序,我们确定了一个特异性的肿瘤内微生物组特征,该特征高度预测了接受手术切除的HCC患者的预后。具体而言,肠内生单胞菌、短杆菌和罗氏菌的存在被确定为手术切除HCC患者总生存率的独立危险因素。尽管一些研究表明肝细胞癌(HCC)中存在丰富的细菌,但对肿瘤内微生物组的组成和多样性对HCC患者预后的有利或不利的了解仍然有限。我们的结果表明,在肿瘤组织中可以观察到比在非肿瘤组织中更丰富的细菌。细菌细胞壁成分与肿瘤相关免疫细胞基本一致。长总生存(LOS)组细菌与代谢和细胞因子-细胞因子受体相互作用途径相关,短总生存(SOS)组细菌与促炎和细胞增殖途径相关。值得注意的是,特定的分类群可以独立预测HCC的预后。基于这些发现,肿瘤内微生物组促进了精准医学在临床实践中的应用。
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引用次数: 0
Genome-resolved year-round dynamics reveal a broad range of giant virus microdiversity. 基因组解析的全年动态揭示了广泛的巨型病毒微多样性。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-23 DOI: 10.1128/msystems.01168-24
Yue Fang, Lingjie Meng, Jun Xia, Yasuhiro Gotoh, Tetsuya Hayashi, Keizo Nagasaki, Hisashi Endo, Yusuke Okazaki, Hiroyuki Ogata

Giant viruses are crucial for marine ecosystem dynamics because they regulate microeukaryotic community structure, accelerate carbon and nutrient cycles, and drive the evolution of their hosts through co-evolutionary processes. Previously reported long-term observations revealed that these viruses display seasonal fluctuations in abundance. However, the underlying genetic mechanisms driving such dynamics of these viruses remain largely unknown. In this study, we investigated the dynamics of giant viruses using time-series metagenomes from eutrophic coastal seawater samples collected over 20 months. A newly developed computational pipeline generated 1,065 high-quality genomes covering six major giant virus lineages. These genomic data revealed year-round recovery of the viral community structure at the study site and distinct dynamics of viral populations that were classified as persistent (n = 9), seasonal (n = 389), sporadic (n = 318), or others. By profiling the intra-species nucleotide-resolved microdiversity through read mapping, we also identified year-round recovery dynamics at subpopulation level for viruses classified as persistent or seasonal. Our results further indicated that giant viruses with broader niche breadth tended to exhibit higher levels of microdiversity. We argue that greater microdiversity of viruses likely enhances adaptability and thus survival under the virus-host arms race during prolonged interactions with their hosts.IMPORTANCERecent genome-resolved metagenomic surveys have uncovered the vast genomic diversity of giant viruses, which play significant roles in aquatic ecosystems by acting as bloom terminators and influencing biogeochemical cycles. However, the relationship between the ecological dynamics of giant viruses and underlying genetic structures of viral populations remains unresolved. In this study, we performed deep metagenomic sequencing of seawater samples collected across a time-series from a coastal area in Japan. The results revealed a significant positive correlation between microdiversity and temporal persistence of giant virus populations, suggesting that population structure is a crucial factor for adaptation and survival in the interactions with their hosts.

巨型病毒对海洋生态系统动力学至关重要,因为它们调节微真核生物群落结构,加速碳和营养循环,并通过共同进化过程驱动宿主的进化。以前报告的长期观察结果显示,这些病毒的丰度呈现季节性波动。然而,驱动这些病毒这种动态的潜在遗传机制在很大程度上仍然未知。在这项研究中,我们利用收集了20多个月的富营养化沿海海水样本的时间序列宏基因组研究了巨型病毒的动态。一个新开发的计算管道生成了1065个高质量的基因组,涵盖了6个主要的巨型病毒谱系。这些基因组数据揭示了研究地点全年病毒群落结构的恢复以及病毒种群的不同动态,这些病毒种群被分类为持久性(n = 9)、季节性(n = 389)、散发性(n = 318)或其他。通过读图分析种内核苷酸分辨的微多样性,我们还确定了亚种群水平上被分类为持久性或季节性的病毒的全年恢复动态。研究结果进一步表明,生态位宽度越宽的巨型病毒,其微多样性水平越高。我们认为,更大的病毒微多样性可能会增强适应性,从而在与宿主的长期相互作用中在病毒-宿主军备竞赛中存活下来。最近的基因组解析宏基因组调查揭示了巨型病毒的巨大基因组多样性,它们通过充当水华终止者和影响生物地球化学循环在水生生态系统中发挥重要作用。然而,巨型病毒的生态动力学与病毒种群的潜在遗传结构之间的关系仍未得到解决。在这项研究中,我们对从日本沿海地区收集的海水样本进行了深度宏基因组测序。结果显示,巨型病毒种群的微多样性与时间持久性之间存在显著正相关,表明种群结构是与其宿主相互作用中适应和生存的关键因素。
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引用次数: 0
Multi-omic signatures of host response associated with presence, type, and outcome of enterococcal bacteremia. 宿主反应的多组学特征与肠球菌菌血症的存在、类型和结果相关。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 DOI: 10.1128/msystems.01471-24
Charlie Bayne, Dominic McGrosso, Concepcion Sanchez, Leigh-Ana Rossitto, Maxwell Patterson, Carlos Gonzalez, Courtney Baus, Cecilia Volk, Haoqi Nina Zhao, Pieter Dorrestein, Victor Nizet, George Sakoulas, David J Gonzalez, Warren Rose
<p><p>Despite the prevalence and severity of enterococcal bacteremia (EcB), the mechanisms underlying systemic host responses to the disease remain unclear. Here, we present an extensive study that profiles molecular differences in plasma from EcB patients using an unbiased multi-omics approach. We performed shotgun proteomics and metabolomics on 105 plasma samples, including those from EcB patients and healthy volunteers. Comparison between healthy volunteer and EcB-infected patient samples revealed significant disparities in proteins and metabolites involved in the acute phase response, inflammatory processes, and cholestasis. Several features distinguish these two groups with remarkable accuracy. Cross-referencing EcB signatures with those of <i>Staphylococcus aureus</i> bacteremia revealed shared reductions in cholesterol metabolism proteins and differing responses in platelet alpha granule and neutrophil-associated proteins. Characterization of <i>Enterococcus</i> isolates derived from patients facilitated a nuanced comparison between EcB caused by <i>Enterococcus faecalis</i> and <i>Enterococcus faecium,</i> uncovering reduced immunoglobulin abundances in <i>E. faecium</i> cases and features capable of distinguishing the underlying microbe. Leveraging extensive patient metadata, we now have identified features associated with mortality or survival, revealing significant multi-omic differences and pinpointing histidine-rich glycoprotein and fetuin-B as features capable of distinguishing survival status with excellent accuracy. Altogether, this study aims to culminate in the creation of objective risk stratification algorithms-a pivotal step toward enhancing patient management and care. To facilitate the exploration of this rich data source, we provide a user-friendly interface at https://gonzalezlab.shinyapps.io/EcB_multiomics/.</p><p><strong>Importance: </strong><i>Enterococcus</i> infections have emerged as the second most common nosocomial infection, with enterococcal bacteremia (EcB) contributing to thousands of patient deaths annually. To address a lack of detailed understanding regarding the specific systemic response to EcB, we conducted a comprehensive multi-omic evaluation of the systemic host response observed in patient plasma. Our findings reveal significant features in the metabolome and proteome associated with the presence of infection, species differences, and survival outcome. We identified features capable of discriminating EcB infection from healthy states and survival from mortality with excellent accuracy, suggesting potential practical clinical utility. However, our study also established that systemic features to distinguish <i>Enterococcus faecalis</i> from <i>Enterococcus faecium</i> EcB show only a moderate degree of discriminatory accuracy, unlikely to significantly improve upon current diagnostic methods. Comparisons of differences in the plasma proteome relative to healthy samples between bacteremia caused by <i>
尽管肠球菌菌血症(EcB)的流行和严重程度,但系统宿主对该疾病反应的机制尚不清楚。在这里,我们提出了一项广泛的研究,利用无偏倚的多组学方法分析了欧洲央行患者血浆中的分子差异。我们对105份血浆样本进行了鸟枪蛋白质组学和代谢组学分析,包括来自欧洲央行患者和健康志愿者的血浆样本。在健康志愿者和感染了eb病毒的患者样本之间进行比较,发现在参与急性期反应、炎症过程和胆汁淤积的蛋白质和代谢物方面存在显著差异。有几个特征非常准确地区分了这两类人。交叉对照EcB特征与金黄色葡萄球菌菌血症的特征显示胆固醇代谢蛋白的共同减少和血小板α颗粒和中性粒细胞相关蛋白的不同反应。从患者身上提取的肠球菌分离物的特征有助于对粪肠球菌和屎肠球菌引起的EcB进行细微的比较,揭示了粪肠球菌病例中免疫球蛋白丰度的降低以及能够区分潜在微生物的特征。利用广泛的患者元数据,我们现在已经确定了与死亡率或生存率相关的特征,揭示了显著的多组学差异,并确定了富组氨酸糖蛋白和胎儿蛋白b作为能够以极高的准确性区分生存状态的特征。总之,本研究旨在最终建立客观的风险分层算法,这是加强患者管理和护理的关键一步。为了方便探索这一丰富的数据源,我们在https://gonzalezlab.shinyapps.io/EcB_multiomics/.Importance上提供了一个用户友好的界面:肠球菌感染已成为第二大常见的医院感染,肠球菌菌血症(EcB)每年导致数千名患者死亡。为了解决对EcB特异性全身反应缺乏详细了解的问题,我们对患者血浆中观察到的全身宿主反应进行了全面的多组学评估。我们的研究结果揭示了与感染、物种差异和生存结果相关的代谢组和蛋白质组的显著特征。我们确定了能够区分EcB感染和健康状态以及生存和死亡的特征,具有很高的准确性,这表明了潜在的实际临床应用价值。然而,我们的研究也证实,区分粪肠球菌和粪肠球菌EcB的系统性特征只有中等程度的区分准确性,不太可能在目前的诊断方法上有显著提高。比较由肠球菌和金黄色葡萄球菌引起的菌血症与健康样本的血浆蛋白质组差异表明,除了保守的炎症反应外,还存在细菌特异性反应。
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引用次数: 0
Correction for Brennan et al., "Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution". 对Brennan等人的更正,“通过基于读取计数分布的精确规范化最大化高通量下一代测序的潜力”。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-13 DOI: 10.1128/msystems.01288-24
Caitriona Brennan, Rodolfo A Salido, Pedro Belda-Ferre, MacKenzie Bryant, Charles Cowart, Maria D Tiu, Antonio Gonzalez, Daniel McDonald, Caitlin Tribelhorn, Amir Zarrinpar, Rob Knight
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引用次数: 0
Multi-omics analysis reveals the interplay between intratumoral bacteria and glioma. 多组学分析揭示了瘤内细菌与胶质瘤之间的相互作用。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-11 DOI: 10.1128/msystems.00457-24
Ting Li, Zhanyi Zhao, Meichang Peng, Lu Zhang, Cheng Wang, Feiyang Luo, Meiqin Zeng, Kaijian Sun, Zhencheng Fang, Yunhao Luo, Yugu Xie, Cui Lv, Jiaxuan Wang, Jian-Dong Huang, Hongwei Zhou, Haitao Sun

Emerging evidence highlights the potential impact of intratumoral microbiota on cancer. However, the microbial composition and function in glioma remains elusive. Consequently, our study aimed to investigate the microbial community composition in glioma tissues and elucidate its role in glioma development. We parallelly performed microbial profiling, transcriptome sequencing, and metabolomics detection on tumor and adjacent normal brain tissues obtained from 50 glioma patients. We employed immunohistochemistry, multicolor immunofluorescence, and fluorescence in situ hybridization (FISH) staining to observe the presence and location of bacteria. Furthermore, an animal model was employed to validate the impact of key bacteria on glioma development. Six genera were found to be significantly enriched in glioma tissues compared to adjacent normal brain tissues, including Fusobacterium, Longibaculum, Intestinimonas, Pasteurella, Limosilactobacillus, and Arthrobacter. Both bacterial RNA and lipopolysaccharides (LPS) were observed in glioma tissues. Integrated microbiomics, transcriptomics, and metabolomics revealed that genes associated with intratumoral microbes were enriched in multiple synapse-associated pathways and that metabolites associated with intratumoral microbes were (R)-N-methylsalsolinol, N-acetylaspartylglutamic acid, and N-acetyl-l-aspartic acid. Further mediation analysis suggested that the intratumoral microbiome may affect the expression of neuron-related genes through bacteria-associated metabolites. In addition, both in vivo and in vitro models of glioma show that Fusobacterium nucleatum promotes glioma proliferation and upregulates CCL2, CXCL1, and CXCL2 levels. Our findings shed light on the intricate interplay between intratumoral bacteria and glioma.

Importance: Our study adopted a multi-omics approach to unravel the impact of intratumoral microbes on neuron-related gene expression through bacteria-associated metabolites. Importantly, we found bacterial RNA and LPS signals within glioma tissues, which were traditionally considered sterile. We identified key microbiota within glioma tissues, including Fusobacterium nucleatum (Fn). Through in vivo and in vitro experiments, we identified the crucial role of Fn in promoting glioma progression, suggesting that Fn could be a potential diagnostic and therapeutic target for glioma patients. These findings offer valuable insights into the intricate interplay between intratumoral bacteria and glioma, offering novel inspiration to the realm of glioma biology.

新出现的证据强调了肿瘤内微生物群对癌症的潜在影响。然而,神经胶质瘤中微生物的组成和功能尚不清楚。因此,我们的研究旨在研究胶质瘤组织中的微生物群落组成,并阐明其在胶质瘤发展中的作用。我们同时对50例胶质瘤患者的肿瘤和邻近正常脑组织进行了微生物谱分析、转录组测序和代谢组学检测。我们采用免疫组织化学、多色免疫荧光和荧光原位杂交(FISH)染色观察细菌的存在和位置。此外,采用动物模型验证关键细菌对胶质瘤发育的影响。与邻近的正常脑组织相比,在胶质瘤组织中发现了6个属的显著富集,包括梭杆菌、长杆菌、无肠单胞菌、巴氏杆菌、乳酸杆菌和节杆菌。在胶质瘤组织中观察到细菌RNA和脂多糖(LPS)。综合微生物组学、转录组学和代谢组学发现,与肿瘤内微生物相关的基因在多种突触相关通路中富集,与肿瘤内微生物相关的代谢物是(R)- n -甲基沙索林醇、n -乙酰天冬氨酸和n -乙酰天冬氨酸。进一步的中介分析表明,肿瘤内微生物组可能通过细菌相关代谢物影响神经元相关基因的表达。此外,胶质瘤的体内和体外模型均显示,核梭杆菌促进胶质瘤增殖,上调CCL2、CXCL1和CXCL2水平。我们的发现揭示了肿瘤内细菌和胶质瘤之间复杂的相互作用。重要性:我们的研究采用多组学方法,通过细菌相关代谢物揭示肿瘤内微生物对神经元相关基因表达的影响。重要的是,我们在胶质瘤组织中发现了细菌RNA和LPS信号,而胶质瘤组织通常被认为是无菌的。我们确定了胶质瘤组织中的关键微生物群,包括核梭杆菌(Fn)。通过体内和体外实验,我们发现Fn在促进胶质瘤进展中的关键作用,提示Fn可能是胶质瘤患者潜在的诊断和治疗靶点。这些发现为瘤内细菌和胶质瘤之间复杂的相互作用提供了有价值的见解,为胶质瘤生物学领域提供了新的灵感。
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引用次数: 0
First-year dynamics of the anaerobic microbiome and archaeome in infants' oral and gastrointestinal systems. 婴儿口腔和胃肠系统中厌氧微生物群和古菌群的第一年动态。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-23 DOI: 10.1128/msystems.01071-24
Charlotte J Neumann, Rokhsareh Mohammadzadeh, Pei Yee Woh, Tanja Kobal, Manuela-Raluca Pausan, Tejus Shinde, Victoria Haid, Polona Mertelj, Eva-Christine Weiss, Vassiliki Kolovetsiou-Kreiner, Alexander Mahnert, Christina Kumpitsch, Evelyn Jantscher-Krenn, Christine Moissl-Eichinger

Recent research provides new insights into the early establishment of the infant gut microbiome, emphasizing the influence of breastfeeding on the development of gastrointestinal microbiomes. In our study, we longitudinally examined the taxonomic and functional dynamics of the oral and gastrointestinal tract (GIT) microbiomes of healthy infants (n = 30) in their first year, focusing on the often-over-looked aspects, the development of archaeal and anaerobic microbiomes. Breastfed (BF) infants exhibit a more defined transitional phase in their oral microbiome compared to non-breastfed (NBF) infants, marked by a decrease in Streptococcus and the emergence of anaerobic genera such as Granulicatella. This phase, characterized by increased alpha-diversity and significant changes in beta-diversity, occurs earlier in NBF infants (months 1-3) than in BF infants (months 4-6), suggesting that breastfeeding supports later, more defined microbiome maturation. We demonstrated the presence of archaea in the infant oral cavity and GIT microbiome from early infancy, with Methanobrevibacter being the predominant genus. Still, transient patterns show that no stable archaeome is formed. The GIT microbiome exhibited gradual development, with BF infants showing increased diversity and complexity between the third and eighth months, marked by anaerobic microbial networks. NBF infants showed complex microbial co-occurrence patterns from the start. These strong differences between BF and NBF infants' GIT microbiomes are less pronounced on functional levels than on taxonomic levels. Overall, the infant microbiome differentiates and stabilizes over the first year, with breastfeeding playing a crucial role in shaping anaerobic microbial networks and overall microbiome maturation.

Importance: The first year of life is a crucial period for establishing a healthy human microbiome. Our study analyses the role of archaea and obligate anaerobes in the development of the human oral and gut microbiome, with a specific focus on the impact of breastfeeding in this process. Our findings demonstrated that the oral and gut microbiomes of breastfed infants undergo distinct phases of increased dynamics within the first year of life. In contrast, the microbiomes of non-breastfed infants are more mature from the first month, leading to a steadier development without distinct transitional phases in the first year. Additionally, we found that archaeal signatures are present in infants under 1 year of age, but they do not form a stable archaeome. In contrast to this, we could track specific bacterial strains transitioning from oral to gut or persisting in the gut over time.

最近的研究为婴儿肠道微生物群的早期建立提供了新的见解,强调了母乳喂养对胃肠道微生物群发育的影响。在我们的研究中,我们纵向检查了健康婴儿(n = 30)一岁时口腔和胃肠道(GIT)微生物群的分类和功能动态,重点关注了经常被忽视的方面,古菌和厌氧微生物群的发展。与非母乳喂养的婴儿相比,母乳喂养的婴儿在口腔微生物群中表现出更明确的过渡阶段,其特征是链球菌的减少和厌氧菌(如颗粒菌)的出现。这一阶段以α -多样性增加和β -多样性显著变化为特征,在非BF婴儿(1-3个月)中比在BF婴儿(4-6个月)中发生得更早,这表明母乳喂养支持更晚、更明确的微生物群成熟。我们证实了婴儿口腔中存在古细菌和婴儿期早期的胃肠道微生物群,其中甲烷杆菌是优势属。然而,瞬时模式表明没有形成稳定的古菌群。胃肠道微生物群逐渐发育,BF婴儿在第3 - 8个月间表现出多样性和复杂性的增加,以厌氧微生物网络为标志。NBF婴儿从一开始就表现出复杂的微生物共生模式。在功能水平上,BF和NBF婴儿GIT微生物组之间的这些强烈差异不如在分类水平上明显。总体而言,婴儿微生物组在第一年分化和稳定,母乳喂养在形成厌氧微生物网络和整体微生物组成熟中起着至关重要的作用。重要性:生命的第一年是建立健康人体微生物群的关键时期。我们的研究分析了古细菌和专性厌氧菌在人类口腔和肠道微生物群发育中的作用,并特别关注母乳喂养对这一过程的影响。我们的研究结果表明,母乳喂养的婴儿的口腔和肠道微生物组在生命的第一年经历了不同的动态增加阶段。相比之下,非母乳喂养婴儿的微生物组从第一个月开始就更加成熟,导致第一年的发育更加稳定,没有明显的过渡阶段。此外,我们发现在1岁以下的婴儿中存在古菌特征,但它们不能形成稳定的古菌群。与此相反,我们可以追踪特定的细菌菌株从口腔过渡到肠道,或者随着时间的推移在肠道中持续存在。
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引用次数: 0
Uncovering novel functions of the enigmatic, abundant, and active Anaerolineae in a salt marsh ecosystem. 揭示了盐沼生态系统中神秘、丰富、活跃的厌氧菌的新功能。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-23 DOI: 10.1128/msystems.01162-24
Paige E Payne, Loren N Knobbe, Patricia Chanton, Julian Zaugg, Behzad Mortazavi, Olivia U Mason

Anaerolineae, particularly uncultured representatives, are one of the most abundant microbial groups in coastal salt marshes, dominating the belowground rhizosphere, where over half of plant biomass production occurs. However, this class generally remains poorly understood, particularly in a salt marsh context. Here, novel Anaerolineae metagenome-assembled genomes (MAGs) were generated from the salt marsh rhizosphere representing Anaerolineales, Promineifilales, JAAYZQ01, B4-G1, JAFGEY01, UCB3, and Caldilineales orders. Metagenome and metatranscriptome reads were mapped to annotated MAGs, revealing nearly all Anaerolineae encoded and transcribed genes required for oxidation of carbon compounds ranging from simple sugars to complex polysaccharides, fermentation, and carbon fixation. Furthermore, the majority of Anaerolineae expressed genes involved in anaerobic and aerobic respiration and secondary metabolite production. The data revealed that the belowground salt marsh Anaerolineae in the rhizosphere are important players in carbon cycling, including degradation of simple carbon compounds and more recalcitrant plant material, such as cellulose, using a diversity of electron acceptors and represent an unexplored reservoir of novel secondary metabolites.IMPORTANCEGiven that coastal salt marshes are recognized as biogeochemical hotspots, it is fundamentally important to understand the functional role of the microbiome in this ecosystem. In particular, Anaerolineae are abundant members of the salt marsh rhizosphere and have been identified as core microbes, suggesting they play an important functional role. Yet, little is known about the metabolic pathways encoded and expressed in this abundant salt marsh clade. Using an 'omics-based approach, we determined that Anaerolineae are capable of oxidizing a range of carbon compounds, including simple sugars to complex carbon compounds, while also encoding fermentation and carbon fixation. Surprisingly, Anaerolineae encoded and transcribed genes involved in aerobic respiration, which was unexpected given the reduced nature of the salt marsh rhizosphere. Finally, the majority of Anaerolineae appear to be involved in secondary metabolite production, suggesting that this group represents an unexplored reservoir of novel and important secondary metabolites.

厌氧菌(Anaerolineae)是沿海盐沼中最丰富的微生物群之一,特别是未经培养的代表,在地下根际占主导地位,其中超过一半的植物生物量生产发生。然而,人们对这类生物的了解仍然很少,特别是在盐沼环境中。本研究从盐沼根际生成了新的厌氧ineae宏基因组组装基因组(MAGs),分别代表厌氧ineales、珥珥eifilales、JAAYZQ01、B4-G1、JAFGEY01、UCB3和Caldilineales目。Metagenome和mettranscriptome reads被映射到注释的MAGs,揭示了从单糖到复杂多糖,发酵和碳固定等碳化合物氧化所需的几乎所有厌氧菌编码和转录基因。此外,大多数厌氧菌表达了参与厌氧和有氧呼吸以及次生代谢物产生的基因。这些数据表明,根际地下盐沼厌氧菌是碳循环的重要参与者,包括使用多种电子受体降解简单碳化合物和更顽固的植物材料(如纤维素),并代表了尚未开发的新型次生代谢物储存库。鉴于沿海盐沼是公认的生物地球化学热点,了解微生物群在这一生态系统中的功能作用至关重要。特别是厌氧菌是盐沼根际的丰富成员,已被确定为核心微生物,表明它们起着重要的功能作用。然而,人们对这种丰富的盐沼进化枝中编码和表达的代谢途径知之甚少。使用基于组学的方法,我们确定厌氧菌能够氧化一系列碳化合物,包括单糖到复杂的碳化合物,同时也编码发酵和碳固定。令人惊讶的是,厌氧菌编码并转录了与有氧呼吸有关的基因,这在盐沼根际减少的情况下是出乎意料的。最后,大多数厌氧菌似乎参与了次生代谢物的产生,这表明这一群体代表了一个尚未开发的新的重要次生代谢物库。
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引用次数: 0
Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment. 电缆细菌沉积物中候选菌群表达的胞外电子转移基因。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-19 DOI: 10.1128/msystems.01259-24
Jamie J M Lustermans, Mantas Sereika, Laurine D W Burdorf, Mads Albertsen, Andreas Schramm, Ian P G Marshall

Cable bacteria, filamentous sulfide oxidizers that live in sulfidic sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remain mostly uninvestigated. Here, we elucidate the electron exchange capabilities of the bacterial community by coupling metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria over 155 days. We identified candidate flocking bacteria as bacteria containing genes for motility and extracellular electron transfer including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Based on these criteria, 22 MAGs were from candidate flockers, which constituted 21.4% of all 103 MAGs. Of the candidate flocking bacteria, 42.1% expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of metabolically versatile taxonomic groups: 18 genera spread across nine phyla. Our data suggest that cable bacteria in freshwater sediments engage in electric relationships with diverse exoelectrogenic microbes. This community, found in deeper anoxic sediment layers, is involved in sulfur, carbon, and metal (in particular Fe) cycling and indirectly utilizes oxygen here by extracellularly transferring electrons to cable bacteria.

Importance: Cable bacteria are ubiquitous, filamentous bacteria that couple sulfide oxidation to the reduction of oxygen at up to centimeter distances in sediment. Cable bacterial impact extends beyond sulfide oxidation via interactions with other bacteria that flock around cable bacteria and use them as electron acceptor "shortcut" to oxygen. The exact nature of this interspecies electric interaction remained unknown. With metagenomics and metatranscriptomics, we determined what extracellular electron transport processes co-occur with cable bacteria, demonstrating the identity and metabolic capabilities of these potential flockers. In sediments, microbial activities are sharply divided into anaerobic and aerobic processes, with oxygen reaching only millimeters deep. Cable bacteria extend the influence of oxygen to several centimeters, revealing a new class of anaerobic microbial metabolism with cable bacteria as electron acceptors. This fundamentally changes our understanding of sediment microbial ecology with wide-reaching consequences for sulfur, metal (in particular Fe), and carbon cycling in freshwater and marine sediments.

电缆细菌,生活在硫化物沉积物中的丝状硫化物氧化剂,有时与大群游动的细菌有关。有人提出,这些细菌群通过电子穿梭中间体在细胞外将电子传递给电缆细菌,但这些细菌在淡水沉积物中的身份和活性大部分尚未得到研究。在这里,我们通过将宏基因组学和亚转录组学与155天内电缆细菌的16S rRNA扩增子相结合来阐明细菌群落的电子交换能力。我们确定候选的群集细菌是含有运动和细胞外电子转移基因的细菌,包括潜在的细胞外电子穿梭的合成基因:非那嗪和黄素。根据这些标准,22个mag来自候选絮凝体,占所有103个mag的21.4%。在候选菌群中,42.1%表达胞外电子转移基因。所提出的絮凝体属于多种代谢多样的分类群:18个属分布在9个门。我们的数据表明,淡水沉积物中的电缆细菌与多种产电微生物存在电关系。这种群落存在于较深的缺氧沉积层中,参与硫、碳和金属(特别是铁)的循环,并通过细胞外将电子传递给电缆细菌间接利用氧气。重要性:电缆细菌是无处不在的丝状细菌,它们将硫化物氧化与沉积物中高达厘米距离的氧气还原结合在一起。电缆细菌的影响不仅限于硫化物氧化,还包括与聚集在电缆细菌周围的其他细菌的相互作用,这些细菌将电缆细菌作为电子受体进入氧气的“捷径”。这种种间电相互作用的确切性质尚不清楚。通过宏基因组学和亚转录组学,我们确定了与电缆细菌共同发生的细胞外电子传递过程,证明了这些潜在絮凝剂的身份和代谢能力。在沉积物中,微生物活动分为厌氧和好氧过程,氧气只能到达毫米深。电缆菌将氧气的影响扩展到几厘米,揭示了一类以电缆菌为电子受体的厌氧微生物代谢的新现象。这从根本上改变了我们对沉积物微生物生态学的理解,对淡水和海洋沉积物中的硫、金属(特别是铁)和碳循环产生了广泛的影响。
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引用次数: 0
Rapid diagnosis of bacterial vaginosis using machine-learning-assisted surface-enhanced Raman spectroscopy of human vaginal fluids. 使用机器学习辅助的人体阴道液表面增强拉曼光谱快速诊断细菌性阴道病。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-12-10 DOI: 10.1128/msystems.01058-24
Xin-Ru Wen, Jia-Wei Tang, Jie Chen, Hui-Min Chen, Muhammad Usman, Quan Yuan, Yu-Rong Tang, Yu-Dong Zhang, Hui-Jin Chen, Liang Wang

Bacterial vaginosis (BV) is an abnormal gynecological condition caused by the overgrowth of specific bacteria in the vagina. This study aims to develop a novel method for BV detection by integrating surface-enhanced Raman scattering (SERS) with machine learning (ML) algorithms. Vaginal fluid samples were classified as BV positive or BV negative using the BVBlue Test and clinical microscopy, followed by SERS spectral acquisition to construct the data set. Preliminary SERS spectral analysis revealed notable disparities in characteristic peak features. Multiple ML models were constructed and optimized, with the convolutional neural network (CNN) model achieving the highest prediction accuracy at 99%. Gradient-weighted class activation mapping (Grad-CAM) was used to highlight important regions in the images for prediction. Moreover, the CNN model was blindly tested on SERS spectra of vaginal fluid samples collected from 40 participants with unknown BV infection status, achieving a prediction accuracy of 90.75% compared with the results of the BVBlue Test combined with clinical microscopy. This novel technique is simple, cheap, and rapid in accurately diagnosing bacterial vaginosis, potentially complementing current diagnostic methods in clinical laboratories.

Importance: The accurate and rapid diagnosis of bacterial vaginosis (BV) is crucial due to its high prevalence and association with serious health complications, including increased risk of sexually transmitted infections and adverse pregnancy outcomes. Although widely used, traditional diagnostic methods have significant limitations in subjectivity, complexity, and cost. The development of a novel diagnostic approach that integrates SERS with ML offers a promising solution. The CNN model's high prediction accuracy, cost-effectiveness, and extraordinary rapidity underscore its significant potential to enhance the diagnosis of BV in clinical settings. This method not only addresses the limitations of current diagnostic tools but also provides a more accessible and reliable option for healthcare providers, ultimately enhancing patient care and health outcomes.

细菌性阴道病(BV)是一种由阴道内特定细菌过度生长引起的异常妇科疾病。本研究旨在通过将表面增强拉曼散射(SERS)与机器学习(ML)算法相结合,开发一种新的BV检测方法。通过BVBlue测试和临床显微镜对阴道液样本进行BV阳性和BV阴性的分类,并通过SERS光谱采集构建数据集。初步的SERS谱分析显示,特征峰特征存在显著差异。构建并优化了多个ML模型,其中卷积神经网络(CNN)模型的预测准确率最高,达到99%。使用梯度加权类激活映射(Grad-CAM)来突出图像中的重要区域进行预测。此外,对40名BV感染状态未知的参与者采集的阴道液样本的SERS谱进行盲测,与BVBlue Test结合临床显微镜的结果相比,CNN模型的预测准确率为90.75%。这种新技术简单、廉价、快速、准确地诊断细菌性阴道病,有可能补充目前临床实验室的诊断方法。重要性:细菌性阴道病(BV)的准确和快速诊断至关重要,因为它的患病率高,并与严重的健康并发症有关,包括性传播感染的风险增加和不良妊娠结局。传统的诊断方法虽然被广泛使用,但在主观性、复杂性和成本等方面存在明显的局限性。将SERS与ML相结合的新型诊断方法的开发提供了一个有前途的解决方案。CNN模型的高预测精度、成本效益和非凡的速度强调了其在临床环境中增强细菌性阴道炎诊断的巨大潜力。这种方法不仅解决了当前诊断工具的局限性,而且为医疗保健提供者提供了更容易获得和更可靠的选择,最终提高了患者护理和健康结果。
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引用次数: 0
Microbial solutions must be deployed against climate catastrophe. 必须采用微生物解决方案来应对气候灾难。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2025-01-21 Epub Date: 2024-11-11 DOI: 10.1128/msystems.01416-24
Raquel Peixoto, Christian R Voolstra, Lisa Y Stein, Philip Hugenholtz, Joana Falcao Salles, Shady A Amin, Max Häggblom, Ann Gregory, Thulani P Makhalanyane, Fengping Wang, Nadège Adoukè Agbodjato, Yinzhao Wang, Nianzhi Jiao, Jay T Lennon, Antonio Ventosa, Patrik M Bavoil, Virginia Miller, Jack A Gilbert
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引用次数: 0
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