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Hfq-binding small RNA PqsS regulates Pseudomonas aeruginosa pqs quorum sensing system and virulence Hfq结合型小核糖核酸PqsS调控铜绿假单胞菌pqs法定人数感应系统和毒力
IF 9.2 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-11 DOI: 10.1038/s41522-024-00550-4
Tianyuan Jia, Xianbiao Bi, Menglu Li, Chenhui Zhang, Anmin Ren, Shangru Li, Tian Zhou, Yingdan Zhang, Yang Liu, Xue Liu, Yinyue Deng, Bin Liu, Guobao Li, Liang Yang

Pseudomonas aeruginosa is a widespread nosocomial pathogen with a significant to cause both severe planktonic acute and biofilm-related chronic infections. Small RNAs (sRNAs) are noncoding regulatory molecules that are stabilized by the RNA chaperone Hfq to trigger various virulence-related signaling pathways. Here, we identified an Hfq-binding sRNA in P. aeruginosa PAO1, PqsS, which promotes bacterial pathogenicity and pseudomonas quinolone signal quorum sensing (pqs QS) system. Specifically, PqsS enhanced acute bacterial infections by inducing host cell death and promoting rhamnolipid-regulated swarming motility. Meanwhile, PqsS reduced chronic infection traits including biofilm formation and antibiotic resistance. Moreover, PqsS repressed pqsL transcript, increasing PQS levels for pqs QS. A PQS-rich environment promoted PqsS expression, thus forming a positive feedback loop. Furthermore, we demonstrated that the PqsS interacts and destabilizes the pqsL mRNA by recruiting RNase E to drive degradation. These findings provide insights for future research on P. aeruginosa pathogenesis and targeted treatment.

铜绿假单胞菌(Pseudomonas aeruginosa)是一种广泛存在的医院病原体,可引起严重的急性浮游生物感染和与生物膜相关的慢性感染。小 RNA(sRNA)是一种非编码调控分子,可通过 RNA 合子 Hfq 的稳定作用触发各种与毒力相关的信号通路。在这里,我们在铜绿假单胞菌 PAO1 中发现了一种与 Hfq 结合的 sRNA,即 PqsS,它能促进细菌的致病性和假单胞菌喹诺酮信号法定人数感应(pqs QS)系统。具体来说,PqsS 通过诱导宿主细胞死亡和促进鼠李糖脂调控的蜂拥运动,增强了急性细菌感染。同时,PqsS 减少了慢性感染特征,包括生物膜的形成和抗生素耐药性。此外,PqsS抑制了pqsL转录本,增加了pqs QS的PQS水平。富含 PQS 的环境促进了 PqsS 的表达,从而形成了一个正反馈回路。此外,我们还证明了 PqsS 通过招募 RNase E 来驱动降解,从而与 pqsL mRNA 相互作用并破坏其稳定性。这些发现为今后研究铜绿假单胞菌的致病机理和靶向治疗提供了启示。
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引用次数: 0
Transient colonizing microbes promote gut dysbiosis and functional impairment. 短暂定植的微生物会导致肠道菌群失调和功能障碍。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-08 DOI: 10.1038/s41522-024-00561-1
Sunjae Lee, Victoria Meslier, Gholamreza Bidkhori, Fernando Garcia-Guevara, Lucie Etienne-Mesmin, Frederick Clasen, Junseok Park, Florian Plaza Oñate, Haizhuang Cai, Emmanuelle Le Chatelier, Nicolas Pons, Marcela Pereira, Maike Seifert, Fredrik Boulund, Lars Engstrand, Doheon Lee, Gordon Proctor, Adil Mardinoglu, Stéphanie Blanquet-Diot, David Moyes, Mathieu Almeida, S Dusko Ehrlich, Mathias Uhlen, Saeed Shoaie

Species composition of the healthy adult gut microbiota tends to be stable over time. Destabilization of the gut microbiome under the influence of different factors is the main driver of the microbial dysbiosis and subsequent impacts on host physiology. Here, we used metagenomics data from a Swedish longitudinal cohort, to determine the stability of the gut microbiome and uncovered two distinct microbial species groups; persistent colonizing species (PCS) and transient colonizing species (TCS). We validated the continuation of this grouping, generating gut metagenomics data for additional time points from the same Swedish cohort. We evaluated the existence of PCS/TCS across different geographical regions and observed they are globally conserved features. To characterize PCS/TCS phenotypes, we performed bioreactor fermentation with faecal samples and metabolic modeling. Finally, using chronic disease gut metagenome and other multi-omics data, we identified roles of TCS in microbial dysbiosis and link with abnormal changes to host physiology.

健康成年人肠道微生物群的物种组成随着时间的推移趋于稳定。在不同因素的影响下,肠道微生物群的不稳定性是导致微生物菌群失调并进而影响宿主生理机能的主要原因。在这里,我们利用来自瑞典纵向队列的元基因组学数据确定了肠道微生物群的稳定性,并发现了两个不同的微生物物种群:持久定植物种(PCS)和短暂定植物种(TCS)。我们从同一瑞典队列的其他时间点生成了肠道元基因组学数据,验证了这一分组的持续性。我们评估了不同地理区域中 PCS/TCS 的存在情况,并观察到它们是全球一致的特征。为了描述 PCS/TCS 的表型,我们对粪便样本进行了生物反应器发酵,并建立了代谢模型。最后,利用慢性病肠道元基因组和其他多组学数据,我们确定了 TCS 在微生物菌群失调中的作用,以及与宿主生理异常变化的联系。
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引用次数: 0
The eukaryome of modern microbialites reveals distinct colonization across aquatic ecosystems. 现代微生物岩的真核细胞组揭示了水生生态系统中不同的定植情况。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-03 DOI: 10.1038/s41522-024-00547-z
Anthony M Bonacolta, Pieter T Visscher, Javier Del Campo, Richard Allen White Iii

Protists are less studied for their role and diversity in ecosystems. Notably, protists have played and still play an important role in microbialites. Microbialites, or lithified microbial mats, represent the oldest evidence of fossil biofilms (~3.5 Gyr). Modern microbialites may offer a unique proxy to study the potential role of protists within a geological context. We examined protist diversity in freshwater (Kelly and Pavilion Lake in British Columbia, Canada) and marine (Highborne Cay, Bahamas) to hypersaline (Shark Bay, Australia) microbialites to decipher their geomicrobiological role. The freshwater microbialite communities were clearly distinct from their marine and hypersaline counterparts. Chlorophytes had higher numerical abundance in freshwater microbialites; whereas pennate diatoms dominated numerically in marine microbialites. Despite the differences, protists across ecosystems may have adopted similar roles and functions. We suggest a consistent biogeochemical role of protists across microbialites globally; but that salinity may shape protist composition and evolution in these ecosystems.

对原生生物在生态系统中的作用和多样性的研究较少。值得注意的是,原生生物过去和现在都在微生物岩中发挥着重要作用。微生物岩或岩石化微生物垫是化石生物膜(约 3.5 Gyr)的最古老证据。现代微生物岩可能为研究原生生物在地质环境中的潜在作用提供了一个独特的替代物。我们研究了淡水(加拿大不列颠哥伦比亚省的凯利湖和亭子湖)和海洋(巴哈马的海博恩礁)至超盐(澳大利亚的鲨鱼湾)微生物岩中的原生生物多样性,以解读它们在地质微生物学中的作用。淡水微生物岩群落明显有别于海洋和超盐微生物岩群落。在淡水微生物岩中,叶绿藻的数量较多;而在海洋微生物岩中,羽状硅藻在数量上占主导地位。尽管存在差异,但不同生态系统中的原生生物可能具有相似的作用和功能。我们认为,原生生物在全球微生物岩中发挥着一致的生物地球化学作用;但盐度可能会影响这些生态系统中原生生物的组成和进化。
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引用次数: 0
Natural killer cell effector function is critical for host defense against alcohol-associated bacterial pneumonia. 自然杀伤细胞效应功能对于宿主防御酒精相关细菌性肺炎至关重要。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-09-03 DOI: 10.1038/s41522-024-00558-w
Daniel N Villageliu, Kelly C Cunningham, Deandra R Smith, Daren L Knoell, Mason Mandolfo, Todd A Wyatt, Derrick R Samuelson

Alcohol use is an independent risk factor for the development of bacterial pneumonia due, in part, to impaired mucus-facilitated clearance, macrophage phagocytosis, and recruitment of neutrophils. Alcohol consumption is also known to reduce peripheral natural killer (NK) cell numbers and compromise NK cell cytolytic activity, especially NK cells with a mature phenotype. However, the role of innate lymphocytes, such as NK cells during host defense against alcohol-associated bacterial pneumonia is essentially unknown. We have previously shown that indole supplementation mitigates increases in pulmonary bacterial burden and improves pulmonary NK cell recruitment in alcohol-fed mice, which were dependent on aryl hydrocarbon receptor (AhR) signaling. Employing a binge-on-chronic alcohol-feeding model we sought to define the role and interaction of indole and NK cells during pulmonary host defense against alcohol-associated pneumonia. We demonstrate that alcohol dysregulates NK cell effector function and pulmonary recruitment via alterations in two key signaling pathways. We found that alcohol increases transforming growth factor beta (TGF-β) signaling while suppressing AhR signaling. We further demonstrated that NK cells isolated from alcohol-fed mice have a reduced ability to kill Klebsiella pneumoniae. NK cell migratory capacity to chemokines was also significantly altered by alcohol, as NK cells isolated from alcohol-fed mice exhibited preferential migration in response to CXCR3 chemokines but exhibited reduced migration in response to CCR2, CXCR4, and CX3CR1 chemokines. Together this data suggests that alcohol disrupts NK cell-specific TGF-β and AhR signaling pathways leading to decreased pulmonary recruitment and cytolytic activity thereby increasing susceptibility to alcohol-associated bacterial pneumonia.

酗酒是细菌性肺炎发病的一个独立危险因素,部分原因是粘液促进的清除能力、巨噬细胞吞噬能力和中性粒细胞招募能力受损。众所周知,饮酒也会减少外周自然杀伤(NK)细胞的数量,损害 NK 细胞的细胞溶解活性,尤其是具有成熟表型的 NK 细胞。然而,先天性淋巴细胞(如 NK 细胞)在宿主防御酒精相关细菌性肺炎过程中所起的作用基本上是未知的。我们之前已经证明,补充吲哚可以减轻酒精喂养小鼠肺部细菌负荷的增加,并改善肺部 NK 细胞的招募,而这依赖于芳基烃受体(AhR)信号传导。我们采用了一种长期酗酒模型,试图明确吲哚和 NK 细胞在肺部宿主防御酒精相关肺炎过程中的作用和相互作用。我们证明,酒精会通过改变两个关键信号通路来失调 NK 细胞效应功能和肺部招募。我们发现酒精增加了转化生长因子β(TGF-β)信号传导,同时抑制了AhR信号传导。我们进一步证实,从酒精喂养的小鼠体内分离出的 NK 细胞杀死肺炎克雷伯氏菌的能力下降。酒精还显著改变了NK细胞对趋化因子的迁移能力,因为从酒精喂养的小鼠体内分离出的NK细胞对CXCR3趋化因子表现出优先迁移,但对CCR2、CXCR4和CX3CR1趋化因子的迁移能力则有所下降。这些数据共同表明,酒精会破坏 NK 细胞特异性的 TGF-β 和 AhR 信号通路,导致肺募集和细胞溶解活性降低,从而增加对酒精相关细菌性肺炎的易感性。
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引用次数: 0
Spaceflight alters host-gut microbiota interactions. 太空飞行会改变宿主-肠道微生物群的相互作用
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-29 DOI: 10.1038/s41522-024-00545-1
E Gonzalez, M D Lee, B T Tierney, N Lipieta, P Flores, M Mishra, L Beckett, A Finkelstein, A Mo, P Walton, F Karouia, R Barker, R J Jansen, S J Green, S Weging, J Kelliher, N K Singh, D Bezdan, J Galazska, N J B Brereton

The ISS rodent habitat has provided crucial insights into the impact of spaceflight on mammals, inducing symptoms characteristic of liver disease, insulin resistance, osteopenia, and myopathy. Although these physiological responses can involve the microbiome on Earth, host-microbiota interactions during spaceflight are still being elucidated. We explore murine gut microbiota and host gene expression in the colon and liver after 29 and 56 days of spaceflight using multiomics. Metagenomics revealed significant changes in 44 microbiome species, including relative reductions in bile acid and butyrate metabolising bacteria like Extibacter muris and Dysosmobacter welbionis. Functional prediction indicate over-representation of fatty acid and bile acid metabolism, extracellular matrix interactions, and antibiotic resistance genes. Host gene expression described corresponding changes to bile acid and energy metabolism, and immune suppression. These changes imply that interactions at the host-gut microbiome interface contribute to spaceflight pathology and that these interactions might critically influence human health and long-duration spaceflight feasibility.

国际空间站啮齿动物栖息地为了解太空飞行对哺乳动物的影响提供了重要信息,这些啮齿动物会诱发肝病、胰岛素抵抗、骨质疏松和肌病等症状。虽然这些生理反应可能涉及地球上的微生物群,但太空飞行期间宿主与微生物群之间的相互作用仍有待阐明。我们利用多组学技术探索了小鼠在太空飞行 29 天和 56 天后的肠道微生物群以及结肠和肝脏中宿主基因的表达。元基因组学揭示了 44 种微生物群的显著变化,包括胆汁酸和丁酸代谢菌(如 Extibacter muris 和 Dysosmobacter welbionis)的相对减少。功能预测表明,脂肪酸和胆汁酸代谢、细胞外基质相互作用和抗生素耐药性基因的代表性过高。宿主基因表达描述了胆汁酸和能量代谢以及免疫抑制的相应变化。这些变化意味着宿主-肠道微生物组界面的相互作用导致了太空飞行病理学,这些相互作用可能会严重影响人类健康和长期太空飞行的可行性。
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引用次数: 0
The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival. 皮肤微生物组对皮肤 T 细胞淋巴瘤患者进行分层并决定无事件生存期。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-29 DOI: 10.1038/s41522-024-00542-4
Philipp Licht, Nazzareno Dominelli, Johannes Kleemann, Stefan Pastore, Elena-Sophia Müller, Maximilian Haist, Kim Sophie Hartmann, Henner Stege, Matthias Bros, Markus Meissner, Stephan Grabbe, Ralf Heermann, Volker Mailänder

Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin. The role of the skin microbiome for MF development and progression are currently poorly understood. Using shotgun metagenomic profiling, real-time qPCR, and T cell receptor sequencing, we compared lesional and nonlesional skin of 20 MF patients with early and advanced MF. Additionally, we isolated Staphylococcus aureus and other bacteria from MF skin for functional profiling and to study the S. aureus virulence factor spa. We identified a subgroup of MF patients with substantial dysbiosis on MF lesions and concomitant outgrowth of S. aureus on plaque-staged lesions, while the other MF patients had a balanced microbiome on lesional skin. Dysbiosis and S. aureus outgrowth were accompanied by ectopic levels of cutaneous antimicrobial peptides (AMPs), including adaptation of the plaque-derived S. aureus strain. Furthermore, the plaque-derived S. aureus strain showed a reduced susceptibility towards antibiotics and an upregulation of the virulence factor spa, which may activate the NF-κB pathway. Remarkably, patients with dysbiosis on MF lesions had a restricted T cell receptor repertoire and significantly lower event-free survival. Our study highlights the potential for microbiome-modulating treatments targeting S. aureus to prevent MF progression.

真菌病(MF)是皮肤 T 细胞淋巴瘤(CTCL)中最常见的一种,其特点是皮肤中存在克隆性恶性 T 细胞。目前,人们对皮肤微生物组在 MF 发生和发展过程中的作用还知之甚少。我们使用枪式元基因组剖析、实时 qPCR 和 T 细胞受体测序技术,比较了 20 名早期和晚期 MF 患者的病变和非病变皮肤。此外,我们还从 MF 皮肤中分离出了金黄色葡萄球菌和其他细菌,以进行功能分析并研究金黄色葡萄球菌的毒力因子 spa。我们发现有一部分手足口病患者的皮损处存在严重的菌群失调,斑块期皮损处同时有金黄色葡萄球菌生长,而其他手足口病患者的皮损处微生物群平衡。菌群失调和金黄色葡萄球菌生长伴随着皮肤抗菌肽(AMPs)水平的异位,包括斑块衍生的金黄色葡萄球菌菌株的适应。此外,菌斑衍生的金黄色葡萄球菌菌株对抗生素的敏感性降低,毒力因子 spa 上调,这可能会激活 NF-κB 通路。值得注意的是,中耳炎病变上菌群失调的患者T细胞受体谱系受限,无事件生存率明显降低。我们的研究强调了针对金黄色葡萄球菌的微生物组调节疗法在预防 MF 进展方面的潜力。
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引用次数: 0
Diet-microbiome interactions promote enteric nervous system resilience following spinal cord injury. 饮食与微生物组之间的相互作用可促进脊髓损伤后肠道神经系统的恢复能力。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-29 DOI: 10.1038/s41522-024-00556-y
Adam M Hamilton, Lisa Blackmer-Raynolds, Yaqing Li, Sean D Kelly, Nardos Kebede, Anna E Williams, Jianjun Chang, Sandra M Garraway, Shanthi Srinivasan, Timothy R Sampson

Spinal cord injury (SCI) results in numerous systemic dysfunctions, including intestinal dysmotility and enteric nervous system (ENS) atrophy. The ENS has capacity to recover following perturbation, yet intestinal pathologies persist. With emerging evidence demonstrating SCI-induced alterations to gut microbiome composition, we hypothesized that microbiome modulation contributes to post-injury enteric recovery. Here, we show that intervention with the dietary fiber, inulin, prevents SCI-induced ENS atrophy and dysmotility in mice. While SCI-associated microbiomes and specific injury-sensitive gut microbes are not sufficient to modulate intestinal dysmotility after injury, intervention with microbially-derived short-chain fatty acid (SCFA) metabolites prevents ENS dysfunctions in injured mice. Notably, inulin-mediated resilience is dependent on IL-10 signaling, highlighting a critical diet-microbiome-immune axis that promotes ENS resilience post-injury. Overall, we demonstrate that diet and microbially-derived signals distinctly impact ENS survival after traumatic spinal injury and represent a foundation to uncover etiological mechanisms and future therapeutics for SCI-induced neurogenic bowel.

脊髓损伤(SCI)会导致许多全身性功能障碍,包括肠道运动障碍和肠神经系统(ENS)萎缩。肠神经系统在受到干扰后有能力恢复,但肠道病变仍然存在。有新的证据表明 SCI 会引起肠道微生物组组成的改变,因此我们假设微生物组的调节有助于伤后肠道的恢复。在这里,我们展示了使用膳食纤维菊粉进行干预可预防 SCI 诱导的小鼠 ENS 萎缩和运动障碍。虽然 SCI 相关微生物群和特定的损伤敏感性肠道微生物不足以调节损伤后的肠道运动障碍,但用微生物衍生的短链脂肪酸(SCFA)代谢物进行干预可防止损伤小鼠的 ENS 功能障碍。值得注意的是,菊粉介导的恢复能力依赖于IL-10信号传导,凸显了饮食-微生物-免疫轴对促进损伤后耳鼻咽喉神经系统恢复能力的关键作用。总之,我们证明饮食和微生物衍生信号对创伤性脊柱损伤后 ENS 的存活有明显影响,为揭示 SCI 引起的神经源性肠道的病因机制和未来疗法奠定了基础。
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引用次数: 0
Combination of bacteriophages and vancomycin in a co-delivery hydrogel for localized treatment of fracture-related infections. 将噬菌体和万古霉素结合到共给水凝胶中,用于局部治疗骨折相关感染。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-29 DOI: 10.1038/s41522-024-00552-2
Baixing Chen, Luis Ponce Benavente, Marco Chittò, Virginia Post, Caroline Constant, Stephan Zeiter, Pamela Nylund, Matteo D'Este, Mercedes González Moreno, Andrej Trampuz, Jeroen Wagemans, Rob Lavigne, Jolien Onsea, R Geoff Richards, Willem-Jan Metsemakers, T Fintan Moriarty

Fracture-related infections (FRIs), particularly those caused by methicillin-resistant Staphylococcus aureus (MRSA), are challenging to treat. This study designed and evaluated a hydrogel loaded with a cocktail of bacteriophages and vancomycin (1.2 mg/mL). The co-delivery hydrogel showed 99.72% reduction in MRSA biofilm in vitro. The hydrogel released 54% of phages and 82% of vancomycin within 72 h and maintained activity for eight days, in vivo the co-delivery hydrogel with systemic antibiotic significantly reduced bacterial load by 0.99 log10 CFU compared to controls, with active phages detected in tissues at euthanasia (2 × 103 PFU/mL). No phage resistance was detected in the phage treatment groups, and serum neutralization resulted in only a 20% reduction in phage count. In this work, we show that a phage-antibiotic co-delivery system via CMC hydrogel is a promising adjunct to systemic antibiotic therapy for MRSA-induced FRI, highlighting its potential for localized, sustained delivery and improved treatment outcomes.

骨折相关感染(FRI),尤其是由耐甲氧西林金黄色葡萄球菌(MRSA)引起的感染,治疗难度很大。本研究设计并评估了一种装有噬菌体鸡尾酒和万古霉素(1.2 毫克/毫升)的水凝胶。在体外,这种协同给药水凝胶可减少 99.72% 的 MRSA 生物膜。水凝胶在 72 小时内释放了 54% 的噬菌体和 82% 的万古霉素,并在 8 天内保持活性。在体内,与对照组相比,联合给药水凝胶和全身抗生素可显著减少细菌负荷 0.99 log10 CFU,安乐死时可在组织中检测到活性噬菌体(2 × 103 PFU/mL)。噬菌体处理组未检测到噬菌体抗药性,血清中和只导致噬菌体数量减少 20%。在这项工作中,我们证明了通过 CMC 水凝胶的噬菌体-抗生素联合给药系统是治疗 MRSA 引起的 FRI 的一种很有前景的辅助全身抗生素疗法,突出了它在局部持续给药和改善治疗效果方面的潜力。
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引用次数: 0
Massive expansion of the pig gut virome based on global metagenomic mining. 基于全球元基因组挖掘的猪肠道病毒组的大规模扩展。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-29 DOI: 10.1038/s41522-024-00554-0
Jiandui Mi, Xiaoping Jing, Chouxian Ma, Yiwen Yang, Yong Li, Yu Zhang, Ruijun Long, Haixue Zheng

The pig gut virome plays a vital role in the gut microbial ecosystem of pigs. However, a comprehensive understanding of their diversity and a reference database for the virome are currently lacking. To address this gap, we established a Pig Virome Database (PVD) that comprised of 5,566,804 viral contig sequences from 4650 publicly available gut metagenomic samples using a pipeline designated "metav". By clustering sequences, we identified 48,299 viral operational taxonomic units (vOTUs) genomes of at least medium quality, of which 92.83% of which were not found in existing major databases. The majority of vOTUs were identified as Caudoviricetes (72.21%). The PVD database contained a total of 2,362,631 protein-coding genes across the above medium-quality vOTUs genomes that can be used to explore the functional potential of the pig gut virome. These findings highlight the extensive diversity of viruses in the pig gut and provide a pivotal reference dataset for forthcoming research concerning the pig gut virome.

猪肠道病毒组在猪的肠道微生物生态系统中发挥着至关重要的作用。然而,目前还缺乏对其多样性的全面了解和病毒组的参考数据库。为了填补这一空白,我们利用名为 "metav "的管道建立了猪病毒组数据库(PVD),该数据库由 5,566,804 个病毒序列组成,这些序列来自 4650 个公开的肠道元基因组样本。通过对序列进行聚类,我们确定了 48,299 个至少中等质量的病毒操作分类单元(vOTUs)基因组,其中 92.83% 的基因组在现有的主要数据库中找不到。大多数 vOTUs 被鉴定为 Caudoviricetes(72.21%)。PVD 数据库包含上述中等质量 vOTU 基因组中总共 2,362,631 个蛋白质编码基因,可用于探索猪肠道病毒组的功能潜力。这些发现凸显了猪肠道病毒的广泛多样性,为即将开展的猪肠道病毒组研究提供了重要的参考数据集。
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引用次数: 0
Fecal microbiota transplantation influences microbiota without connection to symptom relief in irritable bowel syndrome patients. 粪便微生物群移植可影响肠易激综合征患者的微生物群,但与症状缓解无关。
IF 7.8 1区 生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY Pub Date : 2024-08-28 DOI: 10.1038/s41522-024-00549-x
Anna K Hartikainen, Jonna Jalanka, Perttu Lahtinen, Alise J Ponsero, Tuomas Mertsalmi, Laura Finnegan, Fiona Crispie, Paul D Cotter, Perttu Arkkila, Reetta Satokari

Imbalanced microbiota may contribute to the pathophysiology of irritable bowel syndrome (IBS), thus fecal microbiota transplantation (FMT) has been suggested as a potential treatment. Previous studies on the relationship between clinical improvement and microbiota after FMT have been inconclusive. In this study, we used 16S rRNA gene amplicon and shotgun metagenomics data from a randomized, placebo controlled FMT trial on 49 IBS patients to analyze changes after FMT in microbiota composition and its functional potential, and to identify connections between microbiota and patients' clinical outcome. As a result, we found that the successful modulation of microbiota composition and functional profiles by FMT from a healthy donor was not associated with the resolution of symptoms in IBS patients. Notably, a donor derived strain of Prevotella copri dominated the microbiota in those patients in the FMT group who had a low relative abundance of P. copri pre-FMT. The results highlight the multifactorial nature of IBS and the role of recipient's microbiota in the colonization of donor's strains.

微生物群失衡可能是肠易激综合征(IBS)的病理生理学原因之一,因此粪便微生物群移植(FMT)被认为是一种潜在的治疗方法。以往关于 FMT 后临床改善与微生物群之间关系的研究尚无定论。在本研究中,我们利用对 49 名肠易激综合征患者进行的随机安慰剂对照 FMT 试验中的 16S rRNA 基因扩增片段和枪式元基因组学数据,分析了 FMT 后微生物群组成的变化及其功能潜力,并确定了微生物群与患者临床结果之间的联系。结果我们发现,通过对健康供体的 FMT 成功调节微生物群的组成和功能特征与肠易激综合征患者症状的缓解无关。值得注意的是,在 FMT 组中,供体来源的 copri Prevotella 菌株在微生物群中占主导地位,而 FMT 前 copri P. 的相对丰度较低。这些结果突显了肠易激综合征的多因素性质,以及受体微生物群在供体菌株定植中的作用。
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引用次数: 0
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npj Biofilms and Microbiomes
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