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A temperature-induced metabolic shift in the emerging human pathogen Photorhabdus asymbiotica. 新出现的人类病原体 Photorhabdus asymbiotica 的温度诱导代谢转变。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-19 Epub Date: 2024-10-24 DOI: 10.1128/msystems.00970-23
Elena Lucy Carter, Nicholas R Waterfield, Chrystala Constantinidou, Mohammad Tauqeer Alam

Photorhabdus is a bacterial genus containing both insect and emerging human pathogens. Most insect-restricted species display temperature restriction, unable to grow above 34°C, while Photorhabdus asymbiotica can grow at 37°C to infect mammalian hosts and cause Photorhabdosis. Metabolic adaptations have been proposed to facilitate the survival of this pathogen at higher temperatures, yet the biological mechanisms underlying these are poorly understood. We have reconstructed an extensively manually curated genome-scale metabolic model of P. asymbiotica (iEC1073, BioModels ID MODEL2309110001), validated through in silico gene knockout and nutrient utilization experiments with an excellent agreement between experimental data and model predictions. Integration of iEC1073 with transcriptomics data obtained for P. asymbiotica at temperatures of 28°C and 37°C allowed the development of temperature-specific reconstructions representing metabolic adaptations the pathogen undergoes when shifting to a higher temperature in a mammalian compared to insect host. Analysis of these temperature-specific reconstructions reveals that nucleotide metabolism is enriched with predicted upregulated and downregulated reactions. iEC1073 could be used as a powerful tool to study the metabolism of P. asymbiotica, in different genetic or environmental conditions.

Importance: Photorhabdus bacterial species contain both human and insect pathogens, and most of these species cannot grow in higher temperatures. However, Photorhabdus asymbiotica, which infects both humans and insects, can grow in higher temperatures and undergoes metabolic adaptations at a temperature of 37°C compared to that of insect body temperature. Therefore, it is important to examine how this bacterial species can metabolically adapt to survive in higher temperatures. In this work, using a mathematical model, we have examined the metabolic shift that takes place when the bacteria switch from growth conditions in 28°C to 37°C. We show that P. asymbiotica potentially experiences predicted temperature-induced metabolic adaptations at 37°C predominantly clustered within the nucleotide metabolism pathway.

光habdus 是一种细菌属,包含昆虫病原体和新出现的人类病原体。大多数受昆虫限制的物种显示出温度限制,无法在 34°C 以上的温度下生长,而光照杆菌(Photorhabdus asymbiotica)可以在 37°C 的温度下生长,感染哺乳动物宿主并引起光照病。有人提出新陈代谢适应性有助于这种病原体在较高温度下生存,但人们对这些适应性背后的生物机制知之甚少。我们重建了一个经过大量人工编辑的 P. asymbiotica 基因组尺度代谢模型(iEC1073,BioModels ID MODEL2309110001),并通过硅基因敲除和营养物质利用实验进行了验证,实验数据与模型预测结果非常吻合。将 iEC1073 与 P. asymbiotica 在 28°C 和 37°C 温度条件下获得的转录组学数据相结合,可以建立温度特异性重构,代表病原体在哺乳动物宿主中转移到比昆虫宿主更高的温度时所经历的代谢适应性。对这些温度特异性重建的分析表明,核苷酸代谢富含预测的上调和下调反应:重要意义:光habdus 细菌物种中既有人类病原体,也有昆虫病原体,其中大多数物种无法在较高温度下生长。然而,同时感染人类和昆虫的Photorhabdus asymbiotica却能在较高温度下生长,并在37°C的温度下与昆虫体温相比发生新陈代谢适应性变化。因此,研究这种细菌如何进行新陈代谢适应以在更高温度下生存非常重要。在这项工作中,我们利用数学模型研究了细菌从 28°C 生长条件转换到 37°C 生长条件时发生的代谢转变。我们发现,P. asymbiotica 在 37 摄氏度时可能会出现预测的温度诱导代谢适应性变化,这种变化主要集中在核苷酸代谢途径中。
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引用次数: 0
Pooled analysis of oral microbiome profiles defines robust signatures associated with periodontitis. 对口腔微生物组图谱的汇总分析确定了与牙周炎相关的强健特征。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-19 Epub Date: 2024-10-24 DOI: 10.1128/msystems.00930-24
Assem Soueidan, Katia Idiri, Camille Becchina, Pauline Esparbès, Arnaud Legrand, Quentin Le Bastard, Emmanuel Montassier

Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Obtaining these signatures would significantly enhance our understanding of the underlying pathophysiological processes of this condition and foster the development of improved therapeutic strategies, potentially personalized to individual patients. Here, we sequenced newly collected samples from 24 patients with periodontitis, and we collected available oral microbiome data from 24 samples in patients with periodontitis and from 214 samples in healthy individuals (n = 262). Data were harmonized, and we performed a pooled analysis of individual patient data. By metagenomic sequencing of the plaque microbiome, we found microbial signatures for periodontitis and defined a periodontitis-related complex, composed by the most discriminative bacteria. A simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, was associated with periodontitis with high accuracy (area under the curve: 0.94). Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.

Importance: Oral microbial dysbiosis has been associated with periodontitis in studies using 16S rRNA gene sequencing analysis. However, this technology is not sufficient to consistently separate the bacterial species to species level, and reproducible oral microbiome signatures are scarce. Here, using ultra-deep metagenomic sequencing and machine learning tools, we defined a simple two-factor decision tree, based on Tannerella forsythia and Fretibacterium fastidiosum, that was highly associated with periodontitis. Altogether, we defined robust oral microbiome signatures relevant to the pathophysiology of periodontitis that can help define promising targets for microbiome therapeutic modulation when caring for patients with periodontitis.

在使用 16S rRNA 基因测序分析的研究中,口腔微生物菌群失调与牙周炎有关。然而,这项技术还不足以将细菌种类持续分离到物种水平,而且可重复的口腔微生物组特征也很少。获得这些特征将大大提高我们对该病症潜在病理生理过程的了解,促进改善治疗策略的开发,并有可能针对患者个体进行个性化治疗。在此,我们对新收集的 24 名牙周炎患者样本进行了测序,并收集了 24 名牙周炎患者样本和 214 名健康人(n = 262)样本的口腔微生物组数据。我们对数据进行了统一,并对单个患者的数据进行了汇总分析。通过对牙菌斑微生物组进行元基因组测序,我们发现了牙周炎的微生物特征,并定义了由最具鉴别力的细菌组成的牙周炎相关复合菌群。基于连翘坦奈氏菌和快速变形弗氏菌的简单双因子决策树与牙周炎的关联准确率很高(曲线下面积:0.94)。总之,我们定义了与牙周炎病理生理学相关的强大口腔微生物组特征,有助于在护理牙周炎患者时确定有希望的微生物组治疗调节目标:在使用 16S rRNA 基因测序分析的研究中,口腔微生物菌群失调与牙周炎有关。然而,这种技术不足以将细菌种类持续分离到物种水平,而且可重复的口腔微生物组特征也很少。在这里,我们利用超深度元基因组测序和机器学习工具,基于连翘坦奈氏菌和快速变形弗氏菌,定义了一个与牙周炎高度相关的简单双因素决策树。总之,我们定义了与牙周炎病理生理学相关的强大口腔微生物组特征,有助于在护理牙周炎患者时确定有希望的微生物组治疗调节目标。
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引用次数: 0
Correction for Zhu et al., "Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy". 更正 Zhu 等人,"基于匹配参考基因组同时绕过分类学的元基因组群落生态系统发育感知分析"。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-19 Epub Date: 2024-10-18 DOI: 10.1128/msystems.01289-24
Qiyun Zhu, Shi Huang, Antonio Gonzalez, Imran McGrath, Daniel McDonald, Niina Haiminen, George Armstrong, Yoshiki Vázquez-Baeza, Julian Yu, Justin Kuczynski, Gregory D Sepich-Poore, Austin D Swafford, Promi Das, Justin P Shaffer, Franck Lejzerowicz, Pedro Belda-Ferre, Aki S Havulinna, Guillaume Méric, Teemu Niiranen, Leo Lahti, Veikko Salomaa, Ho-Cheol Kim, Mohit Jain, Michael Inouye, Jack A Gilbert, Rob Knight
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引用次数: 0
Phenotypic and genomic characterization of ST11-K1 CR-hvKP with highly homologous blaKPC-2-bearing plasmids in China. 中国带有高度同源 blaKPC-2 质粒的 ST11-K1 CR-hvKP 的表型和基因组特征。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-18 DOI: 10.1128/msystems.01101-24
Yu-Ling Han, Hua Wang, Hong-Zhe Zhu, Ying-Ying Lv, Wen Zhao, Yan-Yan Wang, Jian-Xun Wen, Zhi-De Hu, Jun-Rui Wang, Wen-Qi Zheng

Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) strains present a significant global public health threat due to their high mortality rates. This study investigated the genomic characteristics of seven ST11-K1 CR-hvKP isolates harboring highly homologous KPC-2-encoding multidrug-resistance plasmids. The strains were isolated from a Chinese tertiary hospital between 2017 and 2020. Whole-genome sequencing and bioinformatic analysis revealed various antibiotic resistance genes (ARGs) and virulence determinants. The blaKPC-2-bearing plasmids that contain multiple antibiotic-resistance genes were also identified in these strains. ISfinder and Orifinder were applied to identify insertion sequences (IS) and conjugation-related factors among these blaKPC-2-bearing plasmids. The blaKPC-2 was highly consistent in seven blaKPC-2-bearing plasmids (ISKpn6-blaKPC-2-ISKpn27-ISYps3-IS26). In addition, we found a region composed of ISIR, Tn5393, and IS26. It was located upstream of the blaCTX-M-15 gene and presented in six blaKPC-2-bearing plasmids, with pCR-hvKP221-KPC-P3 as an exception. Conjugation experiments demonstrated the horizontal transfer of resistance plasmids pCR-hvKP128-KPC-P1 and pCR-hvKP132-KPC-P1 across species. Notably, pLVPK-like virulence plasmids carrying virulence gene clusters pCR-hvKP173-Vir-P1, and pCR-hvKP221-Vir-P1 were also detected. A fusional plasmid pCR-hvKP221-Vir-P2, which carries virulence gene clusters and ARGs, was also identified. Five CR-hvKP strains displayed enhanced biofilm formation and high virulence in vivo infection models. Phylogenetic and single nucleotide polymorphism (SNP) analyses indicated a close genetic relationship among the isolates, suggesting a subclade. These findings highlight the complex genetic profiles and potential transmission mechanisms of CR-hvKP strains.

Importance: We reported seven CR-hvKP strains all carried a highly homologous blaKPC-2 integrated IncFⅡ-resistant plasmid, and two strains harbored virulence plasmids. Conjugation experiments confirmed the transferability of these plasmids, indicating a potential for resistance spread. Phylogenetic analysis clarified the relationship among the CR-hvKP isolates. This study provides insights into the phenotypic and genomic characteristics of seven ST11-K1 CR-hvKP strains. The high prevalence and potential for local outbreaks emphasize the need for effective control measures.

耐碳青霉烯类药物的高病毒性肺炎克雷伯氏菌(CR-hvKP)菌株因其高死亡率而对全球公共卫生构成重大威胁。本研究调查了 7 株 ST11-K1 CR-hvKP 分离株的基因组特征,这些分离株携带高度同源的 KPC-2 编码多重耐药质粒。这些菌株于 2017 年至 2020 年期间从一家中国三级医院分离出来。全基因组测序和生物信息学分析揭示了各种抗生素耐药基因(ARGs)和毒力决定因子。在这些菌株中还发现了含有多种抗生素耐药基因的 blaKPC-2 质粒。应用 ISfinder 和 Orifinder 在这些含有 blaKPC-2 的质粒中鉴定插入序列(IS)和共轭相关因子。在七个含有 blaKPC-2 的质粒(ISKpn6-blaKPC-2-ISKpn27-ISYps3-IS26)中,blaKPC-2 高度一致。此外,我们还发现了一个由 ISIR、Tn5393 和 IS26 组成的区域。它位于 blaCTX-M-15 基因的上游,出现在六个含有 blaKPC-2 的质粒中,pCR-hvKP221-KPC-P3 是个例外。共轭实验证明了抗性质粒 pCR-hvKP128-KPC-P1 和 pCR-hvKP132-KPC-P1 的跨物种水平转移。值得注意的是,还检测到了携带毒力基因簇 pCR-hvKP173-Vir-P1 和 pCR-hvKP221-Vir-P1 的类 pLVPK 毒力质粒。此外,还发现了携带毒力基因簇和 ARG 的融合质粒 pCR-hvKP221-Vir-P2。五株 CR-hvKP 菌株在体内感染模型中显示出更强的生物膜形成能力和高毒力。系统发育和单核苷酸多态性(SNP)分析表明,这些分离株之间存在密切的遗传关系,表明存在一个亚支系。这些发现凸显了CR-hvKP菌株复杂的遗传特征和潜在的传播机制:我们报告的七株CR-hvKP菌株均携带高度同源的blaKPC-2整合IncFⅡ抗性质粒,其中两株携带毒力质粒。共轭实验证实了这些质粒的可转移性,表明了抗药性传播的可能性。系统发育分析明确了 CR-hvKP 分离物之间的关系。这项研究深入揭示了七株 ST11-K1 CR-hvKP 菌株的表型和基因组特征。高流行率和局部爆发的可能性强调了采取有效控制措施的必要性。
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引用次数: 0
Dispersal shapes compositional and functional diversity in aquatic microbial communities. 散布决定了水生微生物群落的组成和功能多样性。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-18 DOI: 10.1128/msystems.01403-24
Angel Rain-Franco, Alizée Le Moigne, Lucas Serra Moncadas, Marisa O D Silva, Adrian-Stefan Andrei, Jakob Pernthaler

Segregation and mixing shape the structure and functioning of aquatic microbial communities, but their respective roles are challenging to disentangle in field studies. We explored the hypothesis that functional differences and beta diversity among stochastically assembled communities would increase in the absence of dispersal. Contrariwise, we expected biotic selection during homogenizing dispersal to reduce beta and gamma diversity as well as functional variability. This was experimentally addressed by examining the compositional and functional changes of 20 freshwater bacterial assemblages maintained at identical conditions over seven growth cycles for 34 days and subjected to two consecutive dispersal regimes. Initial dispersal limitation generated high beta diversity and led to the repeated emergence of community types that were dominated by particular taxa. Compositional stability and evenness of the community types varied over successive growth cycles, reflecting differences in functional properties. Carbon use efficiency increased during cultivation, with some communities of unique composition outperforming the replicate community types. Homogenizing dispersal led to high compositional similarity and reduced gamma diversity. While a neutral and a competition-based (Elo-rating) model together largely explained community assembly, a pseudomonad disproportionally dominated across communities, possibly due to interaction-related genomic traits. In conclusion, microbial assemblages stochastically generated by dispersal limitation can be gradually "refined" into distinct community types by subsequent deterministic processes. Segregation of communities represented an insurance mechanism for highly productive but competitively weak microbial taxa that were excluded during community coalescence.

Importance: We experimentally assessed the compositional and functional responses of freshwater bacterial assemblages exposed to two consecutive dispersal-related events (dispersal limitation and homogenizing dispersal) under identical growth conditions. While segregation led to a decreased local diversity, high beta diversity sustained regional diversity and functional variability. In contrast, homogenizing dispersal reduced the species pool and functional variability of the metacommunity. Our findings highlight the role of dispersal in regulating both diversity and functional variability of aquatic microbial metacommunities, thereby providing crucial insight to predict changes in ecosystem functioning.

隔离和混合决定了水生微生物群落的结构和功能,但在实地研究中,很难将它们各自的作用区分开来。我们探讨了这样一个假设:在没有分散的情况下,随机组合的群落之间的功能差异和贝塔多样性会增加。与此相反,我们预计在同质化扩散过程中的生物选择会减少β和γ多样性以及功能变异性。我们通过实验研究了 20 个淡水细菌群落的组成和功能变化,这些群落在相同的条件下保持了 7 个生长周期,历时 34 天,并连续经历了两次扩散。最初的扩散限制产生了较高的β多样性,并导致重复出现由特定类群主导的群落类型。群落类型的组成稳定性和均匀性随连续生长周期而变化,反映了功能特性的差异。碳利用效率在培养过程中不断提高,一些具有独特组成的群落优于复制群落类型。均匀分散导致了高度的成分相似性和伽马多样性的降低。虽然中性模型和基于竞争(Elo-rating)的模型在很大程度上共同解释了群落的组成,但一种假单胞菌在各群落中不成比例地占主导地位,这可能是与相互作用相关的基因组特征造成的。总之,由分散限制随机产生的微生物群落可以通过随后的确定性过程逐渐 "完善 "为不同的群落类型。对于在群落凝聚过程中被排除在外的生产力高但竞争能力弱的微生物类群来说,群落分离是一种保险机制:我们通过实验评估了在相同的生长条件下,淡水细菌群落在两次连续的扩散相关事件(扩散限制和同质化扩散)中的组成和功能反应。虽然隔离导致局部多样性降低,但高贝塔多样性维持了区域多样性和功能变异性。与此相反,同质化扩散降低了元群落的物种库和功能变异性。我们的研究结果强调了分散在调节水生微生物元群落多样性和功能变异性方面的作用,从而为预测生态系统功能的变化提供了重要的启示。
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引用次数: 0
Understanding brewing trait inheritance in de novo Lager yeast hybrids. 了解新拉格酵母杂交种的酿造性状遗传。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-12 DOI: 10.1128/msystems.00762-24
Vasni Zavaleta, Laura Pérez-Través, Luis A Saona, Carlos A Villarroel, Amparo Querol, Francisco A Cubillos
<p><p>Hybridization between <i>Saccharomyces cerevisiae</i> and <i>Saccharomyces eubayanus</i> resulted in the emergence of <i>S. pastorianus</i>, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of <i>S. eubayanus</i> parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in <i>S. cerevisiae</i> and <i>S. eubayanus</i>, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The <i>S. cerevisiae</i> parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer <i>S. cerevisiae</i> parental lineages exhibited a volatile compound profile resembling the corresponding <i>S. eubayanus</i> parent. This pattern may result from the dominant inheritance of the <i>S. eubayanus</i> aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer <i>S. cerevisiae</i> lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies.</p><p><strong>Importance: </strong>Our study investigates the principles of lager yeast hybridization between <i>Saccharomyces cerevisiae</i> and <i>Saccharomyces eubayanus</i>. This process gave rise to the lager yeast <i>Saccharomyces pastorianus</i>. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the <i>S. cerevisiae</i> parent, with Beer lineage hybrids adopting aroma characteristics from their <i>S. eubayanus</i> parent. These insights reveal the complex genetic interactions in hybrid yeasts, openin
酿酒酵母(Saccharomyces cerevisiae)和酿酒酵母(Saccharomyces eubayanus)杂交产生了酿酒酵母(S. pastorianus),它是啤酒发酵的一种重要酵母。然而,由于 S. eubayanus 亲本菌株的稀缺,我们对这两个物种之间杂交成功率和杂交活力的了解仍然有限。在此,我们探讨了杂交成功率以及杂交对新形成的拉格杂交种的发酵性能和挥发性化合物特征的影响。通过从两个物种中选择不同品系的候选亲本,我们发现啤酒品系和 PB-2 品系分别在 S. cerevisiae 和 S. eubayanus 中表现出很高的杂交成功率。通过自发二倍体杂交技术(稀有交配)产生的多倍体杂交种显示,三倍体和二倍体比四倍体更普遍。尽管在发酵能力方面没有异交现象,但杂交种表现出了表型变异性,特别是受麦芽三糖消耗量的影响。有趣的是,虽然三倍体表现出更大的表型变异性,但倍性水平与发酵能力并无明显关联。S. cerevisiae 亲本品系主要影响挥发性化合物特征,在香气产生方面存在显著差异。有趣的是,从啤酒酿造菌(S. cerevisiae)亲本品系中产生的杂交种表现出与相应的啤酒酿造菌(S. eubayanus)亲本相似的挥发性化合物特征。这种模式可能是由 S. eubayanus 香气特征的显性遗传造成的,与酒精代谢和乙酸酯合成相关的基因在包括啤酒酿造啤酒 S. cerevisiae 品系的杂交种中过度表达也说明了这一点。我们的研究结果表明,亲本品系与杂交结果之间存在复杂的相互作用,凸显了通过杂交策略创造具有独特酿造特性的酵母菌的潜力:我们的研究调查了酿酒酵母与酿酒酵母杂交的原理。这一过程产生了酿酒酵母牧酵母。通过研究这些新型杂交种在发酵过程中的表现及其产生的香气,我们揭示了酿造性状遗传的基因基础。我们利用来自两个亲本物种的不同菌株和品系,主要是三倍体和二倍体,成功地产生了多倍体杂交种。虽然这些杂交种的发酵能力没有得到提高,但它们表现出了不同的性状,尤其是在利用麦芽三糖(酿造中的一种关键糖分)方面。值得注意的是,这些杂交种的香气特征主要受 S. cerevisiae 亲本的影响,而 Beer 系杂交种则采用了其 S. eubayanus 亲本的香气特征。这些发现揭示了杂交酵母中复杂的基因相互作用,为制造具有理想性状的独特酿酒酵母提供了新的可能性。
{"title":"Understanding brewing trait inheritance in <i>de novo</i> Lager yeast hybrids.","authors":"Vasni Zavaleta, Laura Pérez-Través, Luis A Saona, Carlos A Villarroel, Amparo Querol, Francisco A Cubillos","doi":"10.1128/msystems.00762-24","DOIUrl":"https://doi.org/10.1128/msystems.00762-24","url":null,"abstract":"&lt;p&gt;&lt;p&gt;Hybridization between &lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt; and &lt;i&gt;Saccharomyces eubayanus&lt;/i&gt; resulted in the emergence of &lt;i&gt;S. pastorianus&lt;/i&gt;, a crucial yeast for lager fermentation. However, our understanding of hybridization success and hybrid vigor between these two species remains limited due to the scarcity of &lt;i&gt;S. eubayanus&lt;/i&gt; parental strains. Here, we explore hybridization success and the impact of hybridization on fermentation performance and volatile compound profiles in newly formed lager hybrids. By selecting parental candidates spanning a diverse array of lineages from both species, we reveal that the Beer and PB-2 lineages exhibit high rates of hybridization success in &lt;i&gt;S. cerevisiae&lt;/i&gt; and &lt;i&gt;S. eubayanus&lt;/i&gt;, respectively. Polyploid hybrids were generated through a spontaneous diploid hybridization technique (rare-mating), revealing a prevalence of triploids and diploids over tetraploids. Despite the absence of heterosis in fermentative capacity, hybrids displayed phenotypic variability, notably influenced by maltotriose consumption. Interestingly, ploidy levels did not significantly correlate with fermentative capacity, although triploids exhibited greater phenotypic variability. The &lt;i&gt;S. cerevisiae&lt;/i&gt; parental lineages primarily influenced volatile compound profiles, with significant differences in aroma production. Interestingly, hybrids emerging from the Beer &lt;i&gt;S. cerevisiae&lt;/i&gt; parental lineages exhibited a volatile compound profile resembling the corresponding &lt;i&gt;S. eubayanus&lt;/i&gt; parent. This pattern may result from the dominant inheritance of the &lt;i&gt;S. eubayanus&lt;/i&gt; aroma profile, as suggested by the over-expression of genes related to alcohol metabolism and acetate synthesis in hybrids including the Beer &lt;i&gt;S. cerevisiae&lt;/i&gt; lineage. Our findings suggest complex interactions between parental lineages and hybridization outcomes, highlighting the potential for creating yeasts with distinct brewing traits through hybridization strategies.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Importance: &lt;/strong&gt;Our study investigates the principles of lager yeast hybridization between &lt;i&gt;Saccharomyces cerevisiae&lt;/i&gt; and &lt;i&gt;Saccharomyces eubayanus&lt;/i&gt;. This process gave rise to the lager yeast &lt;i&gt;Saccharomyces pastorianus&lt;/i&gt;. By examining how these novel hybrids perform during fermentation and the aromas they produce, we uncover the genetic bases of brewing trait inheritance. We successfully generated polyploid hybrids using diverse strains and lineages from both parent species, predominantly triploids and diploids. Although these hybrids did not show improved fermentation capacity, they exhibited varied traits, especially in utilizing maltotriose, a key sugar in brewing. Remarkably, the aroma profiles of these hybrids were primarily influenced by the &lt;i&gt;S. cerevisiae&lt;/i&gt; parent, with Beer lineage hybrids adopting aroma characteristics from their &lt;i&gt;S. eubayanus&lt;/i&gt; parent. These insights reveal the complex genetic interactions in hybrid yeasts, openin","PeriodicalId":18819,"journal":{"name":"mSystems","volume":" ","pages":"e0076224"},"PeriodicalIF":5.0,"publicationDate":"2024-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142624254","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
Dissecting the genetic features and evolution of Staphylococcus aureus sequence type 88: a global perspective. 剖析金黄色葡萄球菌序列 88 型的遗传特征和进化:全球视角。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-12 DOI: 10.1128/msystems.01142-24
Ye Jin, Chenyang Gao, Gaoqin Teng, Zhenchao Zhou, Wangxiao Zhou, Man Huang
<p><p><i>Staphylococcus aureus</i> sequence type (ST) 88, encompassing both methicillin-resistant <i>S. aureus</i> (MRSA) and methicillin-sensitive <i>S. aureus</i> (MSSA) phenotypes, is globally prevalent and commonly associated with skin and soft tissue infections. Despite its widespread occurrence, comprehensive genomic studies on this clone remain scarce. In this study, we performed detailed genomic analyses on 130 ST88 isolates derived from severe bloodstream infections alongside 275 publicly available ST88 sequences. Our phylogenetic analysis identified four distinct clades, with evidence suggesting independent evolution and significant clonal expansion of ST88 in China, particularly within clade I, which appeared to have emerged circa 1964. We documented notable interregional, international, and even intercontinental transmission of ST88 isolates. Variability in the distribution of SCC<i>mec</i> and <i>spa</i> types was observed across clades. Our <i>in silico</i> analyses indicated distinct patterns in the distribution of resistance genes, virulence genes, and mobile genetic elements among the clades, with clade I notably harboring the highest prevalence of the intact <i>sraP</i> gene and an independently acquired novel prophage, φST88-1. Conversely, clade IV exhibited deletions within the <i>sasC</i> gene, with certain sub-clades lacking the <i>sdrDE</i> and <i>fnbB</i> genes, underscoring the superior adhesive capabilities of clade I. <i>In vitro</i> experiments confirmed enhanced biofilm formation in clade I isolates, although the levels of hemolysis and cytotoxicity were similar across clades. Pan-genome-wide association study revealed that core SNPs, rather than the accessory genome, are the primary contributors to the diversification of the ST88 clades. These findings enrich our understanding of the genetic foundations underpinning the transmission dynamics and phenotypic diversity of ST88 clones globally.IMPORTANCEUnderstanding the evolution and transmission of <i>Staphylococcus aureus</i> ST88 clones is critically important due to their spread within food, hospital, and community environments, leading to significant health issues. Despite its prevalence, detailed genomic insights into ST88, particularly regarding its diversity and evolutionary dynamics, have been lacking. Our comprehensive genomic analysis of 130 ST88 isolates from severe bloodstream infections, alongside 275 sequences from public databases, significantly advances our understanding of this pathogen. We identified four distinct evolutionary clades, demonstrating the independent evolution and substantial clonal expansion of ST88 in China, as well as its ability to spread across regions and continents. The diversity among the isolates was evident in their unique profiles of <i>SCCmec</i> elements, antibiotic resistance genes, virulence genes, and mobile genetic elements. Our findings underscore the critical role of core genomic variations over accessory elements in d
金黄色葡萄球菌序列类型(ST)88 包括耐甲氧西林金黄色葡萄球菌(MRSA)和甲氧西林敏感金黄色葡萄球菌(MSSA)两种表型,在全球普遍存在,通常与皮肤和软组织感染有关。尽管其广泛存在,但对该克隆的全面基因组研究仍然很少。在本研究中,我们对 130 个来自严重血流感染的 ST88 分离物和 275 个公开的 ST88 序列进行了详细的基因组分析。我们的系统进化分析确定了四个不同的支系,有证据表明 ST88 在中国有独立的进化和显著的支系扩展,尤其是在支系 I 中,该支系似乎出现于 1964 年前后。我们记录了 ST88 分离物在地区间、国际间甚至洲际间的显著传播。在不同支系中,SCCmec 和 spa 类型的分布存在差异。我们的硅学分析表明,各支系之间的抗性基因、毒力基因和移动遗传因子的分布具有不同的模式,其中支系 I 的完整 sraP 基因和独立获得的新型噬菌体 φST88-1 的流行率最高。体外实验证实,虽然各支系的溶血和细胞毒性水平相似,但支系 I 分离物的生物膜形成能力更强。全基因组关联研究显示,核心 SNPs 而非附属基因组是 ST88 支链多样化的主要因素。重要意义由于金黄色葡萄球菌 ST88 克隆在食品、医院和社区环境中传播,导致严重的健康问题,因此了解金黄色葡萄球菌 ST88 克隆的进化和传播至关重要。尽管金黄色葡萄球菌 ST88 普遍存在,但人们一直缺乏对其基因组的详细了解,尤其是对其多样性和进化动态的了解。我们对来自严重血流感染的 130 株 ST88 分离物以及来自公共数据库的 275 个序列进行了全面的基因组分析,大大加深了我们对这种病原体的了解。我们发现了四个不同的进化支系,证明了 ST88 在中国的独立进化和大量克隆扩增,以及跨地区和跨大陆传播的能力。分离株之间的多样性体现在它们独特的 SCCmec 基因、抗生素耐药基因、毒力基因和移动遗传因子上。我们的发现强调了核心基因组变异比附属元件在驱动 ST88 多样化中的关键作用。这种进一步的了解提供了新的见解,可以为更有效的控制策略提供依据,这对制定干预措施以遏制这种可怕病原体的全球传播至关重要。
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引用次数: 0
Genome streamlining of Pseudomonas putida B6-2 for bioremediation. 精简假单胞菌 B6-2 的基因组,用于生物修复。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-12 DOI: 10.1128/msystems.00845-24
Siqing Fan, Hao Ren, Xueni Fu, Xiangyu Kong, Hao Wu, Zhenmei Lu

Microbial transformation is a favored approach for environmental remediation. However, the effectiveness of microbial remediation has been limited by the lack of chassis cells with satisfactory contaminant degradation performance. Pseudomonas putida B6-2, with a wide substrate spectrum and high solvent tolerance, is a chassis strain with great potential for application in environmental remediation. Here, guided by bioinformatic analyses and genome-scale metabolic model (GEM) predictions, we successfully optimized P. putida B6-2 by rationally reducing its nonessential genetic components and generating a more robust genome-streamlined strain, P. putida BGR4. Several improvements were observed compared with the original P. putida B6-2 strain, including a 1.4 × 105-fold increase in electroporation efficiency, an 8.3-fold increase in conjugation efficiency, improved glycerol utilization capability, and increased phenol utilization after heterologous expression of the phenol monooxygenase encoded by dmpKLMNOP. Additionally, P. putida BGR4 exhibited enhanced tolerance to several stressors, including starvation, oxidative stress, and DNA damage. Transcriptomic analysis revealed that genome streamlining led to the upregulation of genes involved in the "carbon metabolism" and "tricarboxylic acid cycle" pathways in P. putida BGR4, which likely contributed to the superior phenotype of P. putida BGR4 in terms of carbon source utilization and contaminant degradation capabilities. Furthermore, the absence of four prophages was identified as a potential cause of the enhanced stress resistance observed in P. putida BGR4. Overall, we developed a combined genome-streamlining strategy involving bioinformatic analyses and GEM predictions and generated a more robust chassis strain, P. putida BGR4, which expands the repertoire of chassis cells for environmental remediation.IMPORTANCEDespite the development of many chassis cells, there is still a lack of robust chassis cells with satisfactory contaminant degradation performance. Targeted genome streamlining is an effective way to provide powerful chassis cells. However, genome streamlining does not always lead to the improved phenotypes of genome-streamlined chassis cells. In this research, a novel procedure that combined bioinformatic analyses and GEM predictions was proposed to guide genome streamlining and predict the effects of genome streamlining. This genome streamlining procedure was successfully applied to Pseudomonas putida B6-2, which was a chassis cell with great potential for application in environmental remediation and resulted in the generation of a more robust chassis cell, P. putida BGR4, thereby providing a superior chassis cell for efficient and sustainable environmental remediation and a valuable framework for guiding the genome streamlining of strains for other applications.

微生物转化是环境修复的首选方法。然而,由于缺乏具有令人满意的污染物降解性能的基质细胞,微生物修复的有效性受到了限制。普氏假单胞菌 B6-2 具有广泛的底物谱和较高的溶剂耐受性,是一种在环境修复中具有巨大应用潜力的基质菌株。在此,我们以生物信息学分析和基因组尺度代谢模型(GEM)预测为指导,通过合理减少非必要的基因成分,成功优化了假单胞菌 B6-2,并产生了一个更强大的基因组精简菌株--假单胞菌 BGR4。与原始的 P. putida B6-2 菌株相比,我们观察到了一些改进,包括电穿孔效率提高了 1.4 × 105 倍,共轭效率提高了 8.3 倍,甘油利用能力提高了,以及异源表达由 dmpKLMNOP 编码的苯酚单加氧酶后苯酚利用率提高了。此外,P. putida BGR4 对饥饿、氧化应激和 DNA 损伤等几种胁迫的耐受性也有所增强。转录组分析表明,基因组精简导致参与 P. putida BGR4 中 "碳代谢 "和 "三羧酸循环 "途径的基因上调,这可能是 P. putida BGR4 在碳源利用和污染物降解能力方面表现出优异表型的原因。此外,四种噬菌体的缺失也是导致 P. putida BGR4 抗逆性增强的潜在原因。总之,我们开发了一种涉及生物信息学分析和 GEM 预测的联合基因组精简策略,并产生了一种更稳健的底盘菌株 P. putida BGR4,从而扩大了用于环境修复的底盘细胞的范围。重要意义尽管开发了许多底盘细胞,但仍然缺乏具有令人满意的污染物降解性能的稳健底盘细胞。有针对性地精简基因组是提供强大底盘细胞的有效方法。然而,基因组精简并不总能改善基因组精简后底盘细胞的表型。本研究提出了一种结合生物信息学分析和 GEM 预测的新程序,用于指导基因组精简和预测基因组精简的效果。该基因组精简程序被成功应用于具有环境修复巨大应用潜力的假单胞菌 B6-2,并产生了更强健的假单胞菌 BGR4,从而为高效和可持续的环境修复提供了一个卓越的底盘细胞,并为指导其他应用菌株的基因组精简提供了一个有价值的框架。
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引用次数: 0
A comprehensive two-hybrid analysis to explore the Legionella pneumophila effector-effector interactome. 探索嗜肺军团菌效应器-效应器相互作用组的综合双杂交分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-11-11 DOI: 10.1128/msystems.01004-24
Harley O'Connor Mount, Malene L Urbanus, Dayag Sheykhkarimli, Atina G Coté, Florent Laval, Georges Coppin, Nishka Kishore, Roujia Li, Kerstin Spirohn-Fitzgerald, Morgan O Petersen, Jennifer J Knapp, Dae-Kyum Kim, Jean-Claude Twizere, Michael A Calderwood, Marc Vidal, Frederick P Roth, Alexander W Ensminger

Legionella pneumophila uses over 300 translocated effector proteins to rewire host cells during infection and create a replicative niche for intracellular growth. To date, several studies have identified L. pneumophila effectors that indirectly and directly regulate the activity of other effectors, providing an additional layer of regulatory complexity. Among these are "metaeffectors," a special class of effectors that regulate the activity of other effectors once inside the host. A defining feature of metaeffectors is direct, physical interaction with a target effector. Metaeffector identification, to date, has depended on phenotypes in heterologous systems and experimental serendipity. Using a multiplexed, recombinant barcode-based yeast two-hybrid technology we screened for protein-protein interactions among all L. pneumophila effectors and 28 components of the Dot/Icm type IV secretion system (>167,000 protein combinations). Of the 52 protein interactions identified by this approach, 44 are novel protein interactions, including 10 novel effector-effector interactions (doubling the number of known effector-effector interactions).

Importance: Secreted bacterial effector proteins are typically viewed as modulators of host activity, entering the host cytosol to physically interact with and modify the activity of one or more host proteins in support of infection. A growing body of evidence suggests that a subset of effectors primarily function to modify the activities of other effectors inside the host. These "effectors of effectors" or metaeffectors are often identified through experimental serendipity during the study of canonical effector function against the host. We previously performed the first global effector-wide genetic interaction screen for metaeffectors within the arsenal of Legionella pneumophila, an intracellular bacterial pathogen with over 300 effectors. Here, using a high-throughput, scalable methodology, we present the first global interaction network of physical interactions between L. pneumophila effectors. This data set serves as a complementary resource to identify and understand both the scope and nature of non-canonical effector activity within this important human pathogen.

嗜肺军团菌在感染过程中利用 300 多种转座效应蛋白重新连接宿主细胞,并为细胞内生长创造一个复制位点。迄今为止,已有几项研究发现嗜肺军团菌效应蛋白可间接或直接调控其他效应蛋白的活性,从而增加了调控的复杂性。其中包括 "元效应器",这是一类特殊的效应器,一旦进入宿主体内就会调节其他效应器的活性。元效应物的一个显著特点是与目标效应物发生直接的物理相互作用。迄今为止,元效应物的鉴定一直依赖于异源系统中的表型和实验的偶然性。利用基于条形码的多重重组酵母双杂交技术,我们筛选了所有嗜肺病毒效应因子与 Dot/Icm IV 型分泌系统 28 个组分(>167,000 个蛋白质组合)之间的蛋白质相互作用。在这种方法确定的 52 种蛋白质相互作用中,44 种是新型蛋白质相互作用,包括 10 种新型效应物-效应物相互作用(使已知效应物-效应物相互作用的数量翻了一番):分泌的细菌效应蛋白通常被视为宿主活性的调节剂,它们进入宿主细胞质与一种或多种宿主蛋白发生物理作用并改变其活性,以支持感染。越来越多的证据表明,一部分效应蛋白的主要功能是改变宿主体内其他效应蛋白的活性。这些 "效应物的效应物 "或元效应物往往是在研究典型效应物对宿主的功能时通过实验偶然发现的。此前,我们在嗜肺军团菌(一种拥有 300 多种效应器的细胞内细菌病原体)的基因库中进行了首次全球效应器范围的基因相互作用筛选,以寻找元效应器。在这里,我们利用一种高通量、可扩展的方法,首次展示了嗜肺军团菌效应子之间物理相互作用的全球相互作用网络。该数据集是一种补充资源,可用于识别和了解这种重要的人类病原体中非典型效应器活动的范围和性质。
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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 : 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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