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Quality traits drive the enrichment of Massilia in the rhizosphere to improve soybean oil content. 质量特性促使根瘤菌大量繁殖,从而提高了大豆的含油量。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-31 DOI: 10.1186/s40168-024-01933-7
Qin Han, Guanghui Zhu, Hongmei Qiu, Mingbo Li, Jiaming Zhang, Xinying Wu, Renhao Xiao, Yan Zhang, Wei Yang, Bing Tian, Lanxi Xu, Jiayang Zhou, Yutong Li, Yueqiang Wang, Yang Bai, Xia Li

Background: Soybean seeds are rich in protein and oil. The selection of varieties that produce high-quality seeds has been one of the priorities of soybean breeding programs. However, the influence of improved seed quality on the rhizosphere microbiota and whether the microbiota is involved in determining seed quality are still unclear. Here, we analyzed the structures of the rhizospheric bacterial communities of 100 soybean varieties, including 53 landraces and 47 modern cultivars, and evaluated the interactions between seed quality traits and rhizospheric bacteria.

Results: We found that rhizospheric bacterial structures differed between landraces and cultivars and that this difference was directly related to their oil content. Seven bacterial families (Sphingomonadaceae, Gemmatimonadaceae, Nocardioidaceae, Xanthobacteraceae, Chitinophagaceae, Oxalobacteraceae, and Streptomycetaceae) were obviously enriched in the rhizospheres of the high-oil cultivars. Among them, Oxalobacteraceae (Massilia) was assembled specifically by the root exudates of high-oil cultivars and was associated with the phenolic acids and flavonoids in plant phenylpropanoid biosynthetic pathways. Furthermore, we showed that Massilia affected auxin signaling or interfered with active oxygen-related metabolism. In addition, Massilia activated glycolysis pathway, thereby promoting seed oil accumulation.

Conclusions: These results provide a solid theoretical basis for the breeding of revolutionary soybean cultivars with desired seed quality and optimal microbiomes and the development of new cultivation strategies for increasing the oil content of seeds. Video Abstract.

背景:大豆种子富含蛋白质和油脂。选育能生产优质种子的品种一直是大豆育种计划的重点之一。然而,种子质量的提高对根瘤菌群的影响以及微生物群是否参与决定种子质量仍不清楚。在此,我们分析了 100 个大豆品种(包括 53 个陆生品种和 47 个现代栽培品种)的根瘤菌群落结构,并评估了种子质量性状与根瘤菌之间的相互作用:结果:我们发现,不同陆生品种和栽培品种的根瘤细菌结构不同,而且这种差异与含油量直接相关。高油栽培品种根瘤菌明显富集了 7 个细菌科(Sphingomonadaceae、Gemmatimonadaceae、Nocardioidaceae、Xanthobacteraceae、Chitinophagaceae、Oxalobacteraceae 和 Streptomycetaceae)。其中,牛杆菌科(Massilia)在高油栽培品种的根渗出物中特别聚集,并与植物苯丙类生物合成途径中的酚酸和类黄酮相关。此外,我们还发现,Massilia 会影响辅酶信号或干扰活性氧相关的新陈代谢。此外,Massilia 还激活了糖酵解途径,从而促进了种子油的积累:这些结果为培育具有理想种子质量和最佳微生物组的革命性大豆栽培品种以及开发提高种子含油量的新栽培策略提供了坚实的理论基础。视频摘要
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引用次数: 0
Eubacterium siraeum suppresses fat deposition via decreasing the tyrosine-mediated PI3K/AKT signaling pathway in high-fat diet-induced obesity. 在高脂饮食诱导的肥胖症中,西来酵母菌通过减少酪氨酸介导的 PI3K/AKT 信号通路抑制脂肪沉积。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-30 DOI: 10.1186/s40168-024-01944-4
Xueshuang Lai, Shuang Liu, Jian Miao, Ran Shen, Zhen Wang, Zhe Zhang, Huanfa Gong, Meng Li, Yuchun Pan, Qishan Wang

Background: Obesity in humans can lead to chronic diseases such as diabetes and cardiovascular disease. Similarly, subcutaneous fat (SCF) in pigs affects feed utilization, and excessive SCF can reduce the feed efficiency of pigs. Therefore, identifying factors that suppress fat deposition is particularly important. Numerous studies have implicated the gut microbiome in pigs' fat deposition, but research into its suppression remains scarce. The Lulai black pig (LL) is a hybrid breed derived from the Laiwu pig (LW) and the Yorkshire pig, with lower levels of SCF compared to the LW. In this study, we focused on these breeds to identify microbiota that regulate fat deposition. The key questions were: Which microbial populations reduce fat in LL pigs compared to LW pigs, and what is the underlying regulatory mechanism?

Results: In this study, we identified four different microbial strains, Eubacterium siraeum, Treponema bryantii, Clostridium sp. CAG:413, and Jeotgalibaca dankookensis, prevalent in both LW and LL pigs. Blood metabolome analysis revealed 49 differential metabolites, including tanshinone IIA and royal jelly acid, known for their anti-adipogenic properties. E. siraeum was strongly correlated with these metabolites, and its genes and metabolites were enriched in pathways linked to fatty acid degradation, glycerophospholipid, and glycerolipid metabolism. In vivo mouse experiments confirmed that E. siraeum metabolites curb weight gain, reduce SCF adipocyte size, increase the number of brown adipocytes, and regulate leptin, IL-6, and insulin secretion. Finally, we found that one important pathway through which E. siraeum inhibits fat deposition is by suppressing the phosphorylation of key proteins in the PI3K/AKT signaling pathway through the reduction of tyrosine.

Conclusions: We compared LW and LL pigs using fecal metagenomics, metabolomics, and blood metabolomics, identifying E. siraeum as a strain linked to fat deposition. Oral administration experiments in mice demonstrated that E. siraeum effectively inhibits fat accumulation, primarily through the suppression of the PI3K/AKT signaling pathway, a critical regulator of lipid metabolism. These findings provide a valuable theoretical basis for improving pork quality and offer insights relevant to the study of human obesity and related chronic metabolic diseases. Video Abstract.

背景:人类肥胖会导致糖尿病和心血管疾病等慢性疾病。同样,猪的皮下脂肪(SCF)也会影响饲料利用率,过多的皮下脂肪会降低猪的饲料效率。因此,确定抑制脂肪沉积的因素尤为重要。大量研究表明,肠道微生物组与猪的脂肪沉积有关,但对其抑制作用的研究仍然很少。鲁莱黑猪(LL)是由莱芜猪(LW)和约克夏猪(Yorkshire pig)杂交而来的品种,与莱芜猪相比,鲁莱黑猪的SCF水平较低。在本研究中,我们以这些猪种为研究对象,以确定调节脂肪沉积的微生物群。关键问题是与低体重猪相比,哪些微生物种群会减少低体重猪的脂肪,其潜在的调节机制是什么?在这项研究中,我们发现了四种不同的微生物菌株,分别是iraeum 幼杆菌、Treponema bryantii、CAG:413 梭状芽孢杆菌和 Jeotgalibaca dankookensis,它们在低体重猪和低体重猪中都很普遍。血液代谢组分析发现了 49 种不同的代谢物,包括丹参酮 IIA 和蜂王浆酸,它们具有抗脂肪生成的特性。E.siraeum与这些代谢物密切相关,其基因和代谢物富集于脂肪酸降解、甘油磷脂和甘油酯代谢的相关途径中。小鼠体内实验证实,E. siraeum代谢物可抑制体重增加,缩小SCF脂肪细胞体积,增加棕色脂肪细胞数量,调节瘦素、IL-6和胰岛素分泌。最后,我们发现未来草抑制脂肪沉积的一个重要途径是通过减少酪氨酸来抑制 PI3K/AKT 信号通路中关键蛋白的磷酸化:我们利用粪便元基因组学、代谢组学和血液代谢组学对低体重猪和低体重猪进行了比较,发现E. siraeum是一种与脂肪沉积有关的菌株。小鼠口服实验表明,E. siraeum能有效抑制脂肪堆积,主要是通过抑制PI3K/AKT信号通路(脂质代谢的关键调节因子)。这些发现为提高猪肉质量提供了宝贵的理论依据,并为人类肥胖症和相关慢性代谢疾病的研究提供了启示。视频摘要。
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引用次数: 0
The coral Oculina patagonica holobiont and its response to confinement, temperature, and Vibrio infections. Oculina patagonica 整体珊瑚及其对封闭、温度和弧菌感染的反应。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-29 DOI: 10.1186/s40168-024-01921-x
Ana-Belen Martin-Cuadrado, Esther Rubio-Portillo, Francesc Rosselló, Josefa Antón

Background: Extensive research on the diversity and functional roles of the microorganisms associated with reef-building corals has been promoted as a consequence of the rapid global decline of coral reefs attributed to climate change. Several studies have highlighted the importance of coral-associated algae (Symbiodinium) and bacteria and their potential roles in promoting coral host fitness and survival. However, the complex coral holobiont extends beyond these components to encompass other entities such as protists, fungi, and viruses. While each constituent has been individually investigated in corals, a comprehensive understanding of their collective roles is imperative for a holistic comprehension of coral health and resilience.

Results: The metagenomic analysis of the microbiome of the coral Oculina patagonica has revealed that fungi of the genera Aspergillus, Fusarium, and Rhizofagus together with the prokaryotic genera Streptomyces, Pseudomonas, and Bacillus were abundant members of the coral holobiont. This study also assessed changes in microeukaryotic, prokaryotic, and viral communities under three stress conditions: aquaria confinement, heat stress, and Vibrio infections. In general, stress conditions led to an increase in Rhodobacteraceae, Flavobacteraceae, and Vibrionaceae families, accompanied by a decrease in Streptomycetaceae. Concurrently, there was a significant decline in both the abundance and richness of microeukaryotic species and a reduction in genes associated with antimicrobial compound production by the coral itself, as well as by Symbiodinium and fungi.

Conclusion: Our findings suggest that the interplay between microeukaryotic and prokaryotic components of the coral holobiont may be disrupted by stress conditions, such as confinement, increase of seawater temperature, or Vibrio infection, leading to a dysbiosis in the global microbial community that may increase coral susceptibility to diseases. Further, microeukaryotic community seems to exert influence on the prokaryotic community dynamics, possibly through predation or the production of secondary metabolites with anti-bacterial activity. Video Abstract.

背景:由于气候变化导致全球珊瑚礁迅速减少,人们开始广泛研究与造礁珊瑚相关的微生物的多样性和功能作用。一些研究强调了珊瑚相关藻类(共生藻类)和细菌的重要性,以及它们在促进珊瑚宿主健康和生存方面的潜在作用。然而,复杂的珊瑚全生物群并不局限于这些成分,还包括其他实体,如原生生物、真菌和病毒。虽然对珊瑚中的每种成分都进行了单独研究,但要全面了解珊瑚的健康和恢复能力,就必须全面了解它们的共同作用:对 Oculina patagonica 珊瑚微生物组的元基因组分析表明,曲霉属、镰刀菌属和根瘤菌属真菌以及链霉菌属、假单胞菌属和芽孢杆菌属原核生物是珊瑚全生物体中的丰富成员。这项研究还评估了在三种压力条件下微核生物、原核生物和病毒群落的变化:水族箱封闭、热应力和弧菌感染。总体而言,应激条件导致罗氏菌科、黄杆菌科和弧菌科细菌增加,而链霉菌科细菌减少。与此同时,微真核细胞物种的丰度和丰富度显著下降,与珊瑚本身以及共生藻和真菌产生抗微生物化合物有关的基因减少:我们的研究结果表明,珊瑚全生物体的微真核细胞和原核细胞之间的相互作用可能会受到压力条件的破坏,如封闭、海水温度升高或弧菌感染,从而导致全球微生物群落的菌群失调,这可能会增加珊瑚对疾病的易感性。此外,微真核生物群落似乎对原核生物群落的动态产生影响,可能是通过捕食或产生具有抗菌活性的次级代谢产物。视频摘要。
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引用次数: 0
Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health. 原生线虫和病原体拮抗细菌相互作用,促进植物健康。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-28 DOI: 10.1186/s40168-024-01947-1
Xu Xu, Renqiang Jiang, Xinling Wang, Shanshan Liu, Menghui Dong, Hancheng Mao, Xingrui Li, Ziyu Ni, Nana Lv, Xuhui Deng, Wu Xiong, Chengyuan Tao, Rong Li, Qirong Shen, Stefan Geisen

Background: Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown.

Results: Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum.

Conclusions: Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. Video Abstract.

背景:施肥方法通过塑造土壤微生物群来控制导致细菌枯萎病的 Ralstonia solanacearum。该微生物群是食物网的起点,其中线虫是微生物群的主要捕食者。然而,线虫与 R. solanacearum 的表现和植物健康之间的多营养联系,以及这些联系如何受到施肥方法的影响,仍是未知数:结果:在此,我们进行了一项田间试验,研究线虫在抑制番茄细菌性萎蔫病中的潜在作用。我们发现,生物有机肥改变了线虫群落的组成,增加了食菌线虫(如原生线虫)的数量。我们还观察到,病原拮抗细菌(如芽孢杆菌)与食菌线虫的数量呈正相关。在随后的实验室和温室实验中,我们证明细菌线虫优先捕食非病原拮抗细菌,而不是芽孢杆菌。这些变化提高了病原拮抗细菌的性能,从而抑制了茄碱菌:总之,食菌线虫可以减少植物病原体的数量,这可能为促进植物健康提供了一种新的保护策略。视频摘要
{"title":"Protorhabditis nematodes and pathogen-antagonistic bacteria interactively promote plant health.","authors":"Xu Xu, Renqiang Jiang, Xinling Wang, Shanshan Liu, Menghui Dong, Hancheng Mao, Xingrui Li, Ziyu Ni, Nana Lv, Xuhui Deng, Wu Xiong, Chengyuan Tao, Rong Li, Qirong Shen, Stefan Geisen","doi":"10.1186/s40168-024-01947-1","DOIUrl":"10.1186/s40168-024-01947-1","url":null,"abstract":"<p><strong>Background: </strong>Fertilization practices control bacterial wilt-causing Ralstonia solanacearum by shaping the soil microbiome. This microbiome is the start of food webs, in which nematodes act as major microbiome predators. However, the multitrophic links between nematodes and the performance of R. solanacearum and plant health, and how these links are affected by fertilization practices, remain unknown.</p><p><strong>Results: </strong>Here, we performed a field experiment under no-, chemical-, and bio-organic-fertilization regimes to investigate the potential role of nematodes in suppressing tomato bacterial wilt. We found that bio-organic fertilizers changed nematode community composition and increased abundances of bacterivorous nematodes (e.g., Protorhabditis spp.). We also observed that pathogen-antagonistic bacteria, such as Bacillus spp., positively correlated with abundances of bacterivorous nematodes. In subsequent laboratory and greenhouse experiments, we demonstrated that bacterivorous nematodes preferentially preyed on non-pathogen-antagonistic bacteria over Bacillus. These changes increased the performance of pathogen-antagonistic bacteria that subsequently suppressed R. solanacearum.</p><p><strong>Conclusions: </strong>Overall, bacterivorous nematodes can reduce the abundance of plant pathogens, which might provide a novel protection strategy to promote plant health. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"221"},"PeriodicalIF":13.8,"publicationDate":"2024-10-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11520073/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142522303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
The role of the oral microbiota in the causal effect of adjunctive antibiotics on clinical outcomes in stage III-IV periodontitis patients. 口腔微生物群在辅助抗生素对 III-IV 期牙周炎患者临床疗效的因果效应中的作用。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-26 DOI: 10.1186/s40168-024-01945-3
Sven Kleine Bardenhorst, Daniel Hagenfeld, Johannes Matern, Karola Prior, Inga Harks, Peter Eickholz, Katrin Lorenz, Ti-Sun Kim, Thomas Kocher, Jörg Meyle, Doğan Kaner, Yvonne Jockel-Schneider, Dag Harmsen, Benjamin Ehmke

Background: Periodontitis, a prevalent chronic inflammatory disease, offers insights into the broader landscape of chronic inflammatory conditions. The progression and treatment outcomes of periodontitis are closely related to the oral microbiota's composition. Adjunctive systemic Amoxicillin 500 mg and Metronidazole 400 mg, often prescribed thrice daily for 7 days to enhance periodontal therapy's efficacy, have lasting effects on the oral microbiome. However, the precise mechanism through which the oral microbiome influences clinical outcomes in periodontitis patients remains debated. This investigation explores the pivotal role of the oral microbiome's composition in mediating the outcomes of adjunctive systemic antibiotic treatment.

Methods: Subgingival plaque samples from 10 periodontally healthy and 163 periodontitis patients from a randomized clinical trial on periodontal therapy were analyzed. Patients received either adjunctive amoxicillin/metronidazole or a placebo after mechanical periodontal treatment. Microbial samples were collected at various intervals up to 26 months post-therapy. Using topic models, we identified microbial communities associated with normobiotic and dysbiotic states, validated with 86 external and 40 internal samples. Logistic regression models evaluated the association between these microbial communities and clinical periodontitis parameters. A Directed Acyclic Graph (DAG) determined the mediating role of oral microbiota in the causal path of antibiotic treatment effects on clinical outcomes.

Results: We identified clear distinctions between dysbiotic and normobiotic microbial communities, differentiating healthy from periodontitis subjects. Dysbiotic states consistently associated with below median %Pocket Probing Depth ≥ 5 mm (OR = 1.26, 95% CI [1.14-1.42]) and %Bleeding on Probing (OR = 1.09, 95% CI [1.00-1.18]). Factors like microbial response to treatment, smoking, and age were predictors of clinical attachment loss progression, whereas sex and antibiotic treatment were not. Further, we showed that the oral microbial treatment response plays a crucial role in the causal effect of antibiotic treatment on clinical treatment outcomes.

Conclusions: The shift towards a normobiotic subgingival microbiome, primarily induced by adjunctive antibiotics, underscores the potential for microbiome-targeted interventions to enhance therapeutic efficacy in chronic inflammatory conditions. This study reaffirms the importance of understanding the oral microbiome's role in periodontal health and paves the way for future research exploring personalized treatment strategies based on individual microbiome profiles. Video Abstract.

背景:牙周炎是一种普遍存在的慢性炎症性疾病,它使人们对更广泛的慢性炎症性疾病有了更深入的了解。牙周炎的进展和治疗效果与口腔微生物群的组成密切相关。阿莫西林 500 毫克和甲硝唑 400 毫克是辅助性全身用药,通常每天三次,连用 7 天,以提高牙周治疗的疗效,对口腔微生物群有持久的影响。然而,口腔微生物组影响牙周炎患者临床疗效的确切机制仍存在争议。本研究探讨了口腔微生物组的组成在调节系统性抗生素辅助治疗效果中的关键作用:方法:分析了一项牙周治疗随机临床试验中 10 名牙周健康患者和 163 名牙周炎患者的龈下菌斑样本。患者在接受机械性牙周治疗后,接受阿莫西林/甲硝唑或安慰剂的辅助治疗。在治疗后 26 个月内的不同时间间隔收集微生物样本。通过使用主题模型,我们确定了与正常生物状态和菌群失调状态相关的微生物群落,并对 86 份外部样本和 40 份内部样本进行了验证。逻辑回归模型评估了这些微生物群落与临床牙周炎参数之间的关联。有向无环图(DAG)确定了口腔微生物群在抗生素治疗对临床结果影响的因果关系中的中介作用:我们发现了菌群失调与正常生物微生物群落之间的明显区别,并将健康人与牙周炎患者区分开来。菌群失调状态与低于中位数的%牙槽探诊深度≥5毫米(OR = 1.26,95% CI [1.14-1.42])和%探诊出血(OR = 1.09,95% CI [1.00-1.18])密切相关。微生物对治疗的反应、吸烟和年龄等因素是临床附着丧失进展的预测因素,而性别和抗生素治疗则不是。此外,我们还发现,口腔微生物治疗反应在抗生素治疗对临床治疗结果的因果效应中起着至关重要的作用:结论:龈下微生物群向正常生物群的转变主要是由辅助抗生素引起的,这凸显了以微生物群为目标的干预措施在提高慢性炎症治疗效果方面的潜力。这项研究再次证实了了解口腔微生物组在牙周健康中的作用的重要性,并为未来研究探索基于个体微生物组特征的个性化治疗策略铺平了道路。视频摘要。
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引用次数: 0
A single-stranded based library preparation method for virome characterization. 基于单链的病毒体特征库制备方法。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s40168-024-01935-5
Xichuan Zhai, Alex Gobbi, Witold Kot, Lukasz Krych, Dennis Sandris Nielsen, Ling Deng

Background: The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent diversity of genome types (dsDNA, ssDNA, dsRNA, and ssRNA) and topologies (linear, circular, or fragments), with subsequently biases associated with current sequencing library preparation methods. To overcome these problems and improve reproducibility and comparability across studies, universal or standardized virome sequencing library construction methods are highly needed in the gut virome study.

Results: We repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA + Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.

Conclusion: We introduce and improve a fast, simple, and efficient ligation-based single-stranded DNA library preparation for gut virome study. This method is compatible with Illumina sequencing platforms and only requires ligation reagents within 3-h library preparation, which is similar or even better than the advanced library preparation method (xGen). We hope this method can be further optimized, validated, and widely used to make gut virome study more comparable and reproducible. Video Abstract.

背景:肠道病毒组是肠道微生物组不可或缺的组成部分,在维持肠道健康方面发挥着至关重要的作用。然而,由于基因组类型(dsDNA、ssDNA、dsRNA 和 ssRNA)和拓扑结构(线性、环状或片段)固有的多样性,以及随后与当前测序文库制备方法相关的偏差,准确描绘整个肠道病毒组具有挑战性。为了克服这些问题,提高各项研究的可重复性和可比性,肠道病毒组研究亟需通用或标准化的病毒组测序文库构建方法:结果:我们将基于连接的单链文库(SSLR)制备方法重新用于病毒组研究。结果:我们将基于连接的单链文库(SSLR)制备方法重新用于病毒组研究,结果表明,SSLR方法在量化病毒DNA基因组(dsDNA和ssDNA)方面表现出卓越的效率,并且在扩增偏差最小化、覆盖率均匀性和组装病毒基因组的完整性方面优于现有的双链(Nextera)和单链(xGen、MDA + Nextera)文库制备方法。SSLR 方法可用于同时制备 DNA 和 RNA 病毒基因组文库。此外,SSLR 方法还能捕获高度修饰的噬菌体基因组,而其他文库制备方法往往会丢失这些基因组:我们介绍并改进了一种用于肠道病毒组研究的快速、简单、高效的基于连接的单链 DNA 文库制备方法。该方法与 Illumina 测序平台兼容,在 3 小时的文库制备过程中只需连接试剂,与先进的文库制备方法(xGen)相似甚至更好。我们希望这种方法能得到进一步优化、验证和广泛应用,使肠道病毒组研究更具可比性和可重复性。视频摘要。
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引用次数: 0
Surface microlayer-mediated virome dissemination in the Central Arctic. 北极中部由表面微层介导的病毒传播。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-24 DOI: 10.1186/s40168-024-01902-0
Janina Rahlff, George Westmeijer, Julia Weissenbach, Alfred Antson, Karin Holmfeldt

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

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

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

背景:水生病毒是形成微生物群落的关键角色。在极地环境中,它们面临着宿主有限和条件恶劣等重大挑战。然而,由于这些生态系统的可及性有限,我们对病毒多样性、丰度、适应性和宿主相互作用的了解仍然有限:为了填补这一知识空白,我们研究了北极中部和格陵兰岛北部与大气接近的水生生态系统中的病毒。在北极夏季奥登号破冰船进行 2021 年北极综合考察期间,我们从约 60 厘米深的水域和亚毫米表面微层(SML)采集了用于病毒宿主分析的水生样本。水样取自熔池和开放水域,然后进行大小分馏过滤,再进行基因组分辨元基因组和培养研究。与开放水域相比,熔池中的原核生物多样性要低得多。熔池中的原核生物主要是黄杆菌和 Aquiluna sp.,后者的基因组相对较小,只有 1.2 Mb,具有利用磷酸乙酰转移酶-乙酸激酶途径产生 ATP 的代谢潜力。与开放水域相比,熔池中宿主部分(0.2-5 微米)的病毒多样性非常有限。在1154个病毒操作分类单元(vOTUs)(其中三分之二是预测的噬菌体)中,17.2%的病毒编码具有代谢功能的辅助代谢基因(AMGs)。一些 AMGs,如甘油-3-磷酸胞苷酸转移酶和类冰结合蛋白,可能为宿主提供低温保护。噬菌体通常与SML基因组相关,北极SML菌株Leeuwenhoekiella aequorea Arc30的两个新病毒属的活性噬菌体被诱导出来。我们发现有证据表明,与 ~60 厘米深度相比,SML 中的 vOTU 丰度与五个不同北极站的 vOTU 分布呈正相关:结论:研究结果表明,病毒采用了精心设计的策略,以在宿主有限的极端环境中生存。此外,我们的观察结果表明,紧邻的海气界面是病毒在北极中部分布的平台。视频摘要
{"title":"Surface microlayer-mediated virome dissemination in the Central Arctic.","authors":"Janina Rahlff, George Westmeijer, Julia Weissenbach, Alfred Antson, Karin Holmfeldt","doi":"10.1186/s40168-024-01902-0","DOIUrl":"10.1186/s40168-024-01902-0","url":null,"abstract":"<p><strong>Background: </strong>Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited.</p><p><strong>Results: </strong>To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2-5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations.</p><p><strong>Conclusions: </strong>The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Video Abstract.</p>","PeriodicalId":18447,"journal":{"name":"Microbiome","volume":"12 1","pages":"218"},"PeriodicalIF":13.8,"publicationDate":"2024-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11515562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142503492","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Metaproteomics reveals diet-induced changes in gut microbiome function according to Crohn's disease location. 元蛋白质组学揭示了根据克罗恩病发病部位饮食诱导的肠道微生物组功能变化。
IF 13.8 1区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-10-23 DOI: 10.1186/s40168-024-01927-5
Stefano Levi Mortera, Valeria Marzano, Federica Rapisarda, Chiara Marangelo, Ilaria Pirona, Pamela Vernocchi, Marta Di Michele, Federica Del Chierico, Maria A Quintero, Irina Fernandez, Hajar Hazime, Rose M Killian, Norma Solis, Mailenys Ortega, Oriana M Damas, Siobhan Proksell, David H Kerman, Amar R Deshpande, Luis Garces, Franco Scaldaferri, Antonio Gasbarrini, Maria T Abreu, Lorenza Putignani

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

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

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

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

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

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

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

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

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

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

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

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

背景:肠道微生物群是骨代谢的关键调节因子。研究肠道微生物群与骨骼重塑之间的关系为治疗骨骼相关疾病提供了新途径。尽管在了解哺乳动物肠道微生物群与骨骼相互作用方面取得了重大进展,但对鸟类物种的研究仍然有限。鸟类具有独特的骨骼解剖和生理结构,以支持产蛋。然而,肠道微生物群是否以及如何影响鸟类的骨骼生理机能仍是未知数。在这项研究中,我们利用蛋鸡作为研究模型,分析骨骼发育模式,阐明骨骼与肠道微生物群之间的关系,并挖掘具有骨调节作用的益生菌:结果:衰老导致蛋鸡股骨中的骨矿物质密度持续增加。老龄蛋鸡骨髓腔中髓质骨的持续沉积导致骨小梁显著流失和骨代谢减弱。性成熟前后盲肠微生物组成发生了显著变化,梭菌属中的一些菌属可能与蛋鸡出生后的骨骼发育有关。在细菌负荷较低的雏鸡和鸡初级成骨细胞中鉴定并评估了与骨骼发育相关的四种细菌菌株,即Blautia coccoides CML164、Fournierella sp002159185 CML151、Anaerostipes caccae CML199(ANA)和Romboutsia lituseburensis CML137。其中,ANA 对体内和体外骨形成的促进作用最为显著,这主要归功于其发酵产物中的丁酸盐。一项长达 72 周的长期饲喂实验证实,ANA 通过改善蛋鸡骨髓的免疫微环境,促进了性成熟期间的骨骼发育。连续 50 周膳食补充 ANA 可防止髓质骨过度沉积,并减轻衰老引起的小梁骨质流失:这些发现强调了 ANA 对骨生理学的有益影响,为基于微生物的家禽骨相关疾病干预提供了新的视角,并可能扩展到人类健康。视频摘要。
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引用次数: 0
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Microbiome
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