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A genome-scale metabolic model of a globally disseminated hyperinvasive M1 strain of Streptococcus pyogenes. 全球传播的高侵袭性化脓性链球菌 M1 株的基因组尺度代谢模型。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-19 DOI: 10.1128/msystems.00736-24
Yujiro Hirose, Daniel C Zielinski, Saugat Poudel, Kevin Rychel, Jonathon L Baker, Yoshihiro Toya, Masaya Yamaguchi, Almut Heinken, Ines Thiele, Shigetada Kawabata, Bernhard O Palsson, Victor Nizet

Streptococcus pyogenes is responsible for a range of diseases in humans contributing significantly to morbidity and mortality. Among more than 200 serotypes of S. pyogenes, serotype M1 strains hold the greatest clinical relevance due to their high prevalence in severe human infections. To enhance our understanding of pathogenesis and discovery of potential therapeutic approaches, we have developed the first genome-scale metabolic model (GEM) for a serotype M1 S. pyogenes strain, which we name iYH543. The curation of iYH543 involved cross-referencing a draft GEM of S. pyogenes serotype M1 from the AGORA2 database with gene essentiality and autotrophy data obtained from transposon mutagenesis-based and growth screens. We achieved a 92.6% (503/543 genes) accuracy in predicting gene essentiality and a 95% (19/20 amino acids) accuracy in predicting amino acid auxotrophy. Additionally, Biolog Phenotype microarrays were employed to examine the growth phenotypes of S. pyogenes, which further contributed to the refinement of iYH543. Notably, iYH543 demonstrated 88% accuracy (168/190 carbon sources) in predicting growth on various sole carbon sources. Discrepancies observed between iYH543 and the actual behavior of living S. pyogenes highlighted areas of uncertainty in the current understanding of S. pyogenes metabolism. iYH543 offers novel insights and hypotheses that can guide future research efforts and ultimately inform novel therapeutic strategies.IMPORTANCEGenome-scale models (GEMs) play a crucial role in investigating bacterial metabolism, predicting the effects of inhibiting specific metabolic genes and pathways, and aiding in the identification of potential drug targets. Here, we have developed the first GEM for the S. pyogenes highly virulent serotype, M1, which we name iYH543. The iYH543 achieved high accuracy in predicting gene essentiality. We also show that the knowledge obtained by substituting actual measurement values for iYH543 helps us gain insights that connect metabolism and virulence. iYH543 will serve as a useful tool for rational drug design targeting S. pyogenes metabolism and computational screening to investigate the interplay between inhibiting virulence factor synthesis and growth.

化脓性链球菌是人类一系列疾病的元凶,严重影响发病率和死亡率。在 200 多种化脓性链球菌血清型中,血清型 M1 菌株因其在严重人类感染中的高流行率而具有最大的临床意义。为了加深我们对致病机理的了解并发现潜在的治疗方法,我们为血清型 M1 化脓性链球菌菌株开发了首个基因组尺度代谢模型(GEM),并将其命名为 iYH543。iYH543 的制作包括将 AGORA2 数据库中的 M1 血清型化脓性链球菌 GEM 草案与基于转座子诱变和生长筛选获得的基因本质和自营养数据进行交叉比对。我们预测基因本质的准确率为 92.6%(503/543 个基因),预测氨基酸营养不良的准确率为 95%(19/20 个氨基酸)。此外,我们还利用 Biolog 表型微阵列检测了化脓性链球菌的生长表型,这进一步促进了 iYH543 的完善。值得注意的是,iYH543 在预测各种唯一碳源上的生长时显示出 88% 的准确率(168/190 碳源)。重要意义基因组尺度模型(GEM)在研究细菌代谢、预测抑制特定代谢基因和途径的效果以及帮助鉴定潜在药物靶点方面发挥着至关重要的作用。在这里,我们开发了第一个针对化脓性链球菌高致病性血清型 M1 的 GEM,并将其命名为 iYH543。iYH543 在预测基因本质方面达到了很高的准确度。我们还表明,用实际测量值代替 iYH543 所获得的知识有助于我们深入了解新陈代谢与毒力之间的关系。iYH543 将成为针对化脓性链球菌新陈代谢的合理药物设计和计算筛选的有用工具,以研究抑制毒力因子合成与生长之间的相互作用。
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引用次数: 0
Decomposing a San Francisco estuary microbiome using long-read metagenomics reveals species- and strain-level dominance from picoeukaryotes to viruses. 利用长读数元基因组学分解旧金山河口微生物组,揭示了从微小核生物到病毒的物种和菌株级优势。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-19 DOI: 10.1128/msystems.00242-24
Lauren M Lui, Torben N Nielsen

Although long-read sequencing has enabled obtaining high-quality and complete genomes from metagenomes, many challenges still remain to completely decompose a metagenome into its constituent prokaryotic and viral genomes. This study focuses on decomposing an estuarine metagenome to obtain a more accurate estimate of microbial diversity. To achieve this, we developed a new bead-based DNA extraction method, a novel bin refinement method, and obtained 150 Gbp of Nanopore sequencing. We estimate that there are ~500 bacterial and archaeal species in our sample and obtained 68 high-quality bins (>90% complete, <5% contamination, ≤5 contigs, contig length of >100 kbp, and all ribosomal and tRNA genes). We also obtained many contigs of picoeukaryotes, environmental DNA of larger eukaryotes such as mammals, and complete mitochondrial and chloroplast genomes and detected ~40,000 viral populations. Our analysis indicates that there are only a few strains that comprise most of the species abundances.

Importance: Ocean and estuarine microbiomes play critical roles in global element cycling and ecosystem function. Despite the importance of these microbial communities, many species still have not been cultured in the lab. Environmental sequencing is the primary way the function and population dynamics of these communities can be studied. Long-read sequencing provides an avenue to overcome limitations of short-read technologies to obtain complete microbial genomes but comes with its own technical challenges, such as needed sequencing depth and obtaining high-quality DNA. We present here new sampling and bioinformatics methods to attempt decomposing an estuarine microbiome into its constituent genomes. Our results suggest there are only a few strains that comprise most of the species abundances from viruses to picoeukaryotes, and to fully decompose a metagenome of this diversity requires 1 Tbp of long-read sequencing. We anticipate that as long-read sequencing technologies continue to improve, less sequencing will be needed.

尽管长线程测序技术已经能够从元基因组中获得高质量的完整基因组,但要将元基因组完全分解为其组成的原核生物和病毒基因组,仍然存在许多挑战。本研究的重点是分解河口元基因组,以便更准确地估计微生物的多样性。为此,我们开发了一种新的基于珠子的 DNA 提取方法和一种新的 bin 细化方法,并获得了 150 Gbp 的 Nanopore 测序结果。我们估计样本中有约 500 个细菌和古细菌物种,并获得了 68 个高质量 bins(>90% 完整、100 kbp、所有核糖体和 tRNA 基因)。我们还获得了许多皮核生物的等位基因、哺乳动物等大型真核生物的环境 DNA 以及完整的线粒体和叶绿体基因组,并检测到约 4 万个病毒种群。我们的分析表明,只有少数菌株构成了大部分物种的丰度:海洋和河口微生物群在全球元素循环和生态系统功能中发挥着关键作用。尽管这些微生物群落非常重要,但许多物种仍未在实验室中培养出来。环境测序是研究这些群落的功能和种群动态的主要方法。长线程测序为克服短线程技术的局限性以获得完整的微生物基因组提供了一条途径,但也带来了自身的技术挑战,如所需的测序深度和获得高质量的 DNA。我们在此介绍新的取样和生物信息学方法,尝试将河口微生物组分解为其组成基因组。我们的研究结果表明,从病毒到皮核生物,只有少数几个菌株组成了大部分物种的丰度,而要完全分解如此多样性的元基因组,需要 1 Tbp 的长线程测序。我们预计,随着长线程测序技术的不断改进,所需的测序量将会减少。
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引用次数: 0
Phenotypic and genomic analysis of the hypervirulent methicillin-resistant Staphylococcus aureus ST630 clone in China. 中国高病毒耐甲氧西林金黄色葡萄球菌 ST630 克隆的表型和基因组分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-19 DOI: 10.1128/msystems.00664-24
Junhong Shi, Yanghua Xiao, Li Shen, Cailing Wan, Bingjie Wang, Peiyao Zhou, Jiao Zhang, Weihua Han, Fangyou Yu

Methicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) is a rarely reported lineage worldwide. This study aimed to trace the dissemination of the emerging MRSA ST630 clones in China and investigate their virulence potential. We collected 22 ST630-MRSA isolates from across China and performed whole-genome sequencing analysis and virulence characterization on these isolates. Epidemiological results showed that MRSA ST630 isolates were primarily isolated from pus/wound secretions, mainly originating from Jiangxi province, and carried diverse virulence and drug resistance genes. Staphylococcal cassette chromosome mec type V (SCCmec V) predominated (11/22, 50.0%) among the MRSA ST630 isolates. Interestingly, nearly half (45.5%) of the 22 ST630-MRSA isolates tested lacked intact SCCmec elements. Phylogenetic analysis demonstrated that ST630-MRSA could be divided into two distinct clades, with widespread dissemination mainly in Chinese regions. Five representative isolates were selected for phenotypic assays, including hemolysin activity, real-time fluorescence quantitative PCR, western blot analysis, hydrogen peroxide killing assay, blood killing assay, cell adhesion and invasion assay, and mouse skin abscess model. The results showed that, compared to the USA300-LAC strain, ST630 isolates exhibited particularly strong invasiveness and virulence in the aforementioned phenotypic assays. This study described the emergence of a highly virulent ST630-MRSA lineage and improved our insight into the molecular epidemiology of ST630 clones in China.IMPORTANCEMethicillin-resistant Staphylococcus aureus (MRSA) sequence type 630 (ST630) is an emerging clone with an increasing isolation rate in China. This study raises awareness of the hypervirulent MRSA ST630 clones in China and alerts people to their widespread dissemination. ST630-staphylococcal cassette chromosome mec V is a noteworthy clone in China, and we present the first comprehensive genetic and phenotypic analysis of this lineage. Our findings provide valuable insights for the prevention and control of infections caused by this emerging MRSA clone.

耐甲氧西林金黄色葡萄球菌(MRSA)序列630型(ST630)是一种全球罕见的菌系。本研究旨在追踪新出现的 MRSA ST630 克隆在中国的传播情况,并研究它们的毒力潜力。我们从中国各地收集了22株ST630-MRSA分离株,并对这些分离株进行了全基因组测序分析和毒力鉴定。流行病学结果显示,MRSA ST630主要分离自脓/伤口分泌物,主要来源于江西省,携带多种毒力和耐药基因。在MRSA ST630分离株中,以金黄色葡萄球菌盒式染色体mec V型(SCCmec V)为主(11/22,50.0%)。有趣的是,在检测的 22 个 ST630-MRSA 分离物中,近一半(45.5%)缺乏完整的 SCCmec 元件。系统发生学分析表明,ST630-MRSA 可分为两个不同的支系,主要在中国地区广泛传播。研究人员选取了五个具有代表性的分离株进行表型分析,包括溶血素活性、实时荧光定量 PCR、Western 印迹分析、过氧化氢杀灭试验、血液杀灭试验、细胞粘附和侵袭试验以及小鼠皮肤脓肿模型。结果表明,与USA300-LAC菌株相比,ST630分离株在上述表型检测中表现出特别强的侵袭性和毒力。本研究描述了高致病性 ST630-MRSA 世系的出现,并提高了我们对中国 ST630 克隆的分子流行病学的认识。本研究提高了人们对中国高病毒MRSA ST630克隆的认识,并提醒人们注意其广泛传播。ST630 葡萄球菌盒式染色体 mec V 是中国值得注意的克隆,我们首次对这一菌株进行了全面的遗传和表型分析。我们的研究结果为预防和控制这种新出现的 MRSA 克隆引起的感染提供了有价值的见解。
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引用次数: 0
Impact of urbanization on gut microbiome mosaics across geographic and dietary contexts 城市化对不同地域和饮食背景下肠道微生物组镶嵌的影响
IF 6.4 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 DOI: 10.1128/msystems.00585-24
Elizaveta VinogradovaNurislam MukhanbetzhanovMadiyar NurgaziyevZharkyn JarmukhanovRakhilya AipovaAliya SailybayevaMakhabbat BekbossynovaSamat KozhakhmetovAlmagul Kushugulova1Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan2Kazakh Research Institute of Soil Science and Agricultural Chemistry named after U.Uspanov, Almaty, Kazakhstan3JSC “National Research Cardiac Surgery Center”, Astana, KazakhstanVanni Bucci
mSystems, Ahead of Print.
mSystems, Ahead of Print.
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引用次数: 0
The developing pig respiratory microbiome harbors strains antagonistic to common respiratory pathogens 发育中的猪呼吸道微生物群蕴藏着拮抗常见呼吸道病原体的菌株
IF 6.4 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 DOI: 10.1128/msystems.00626-24
Abel A. VlasblomBirgitta DuimShriram PatelRoosmarijn E. C. LuikenDaniel Crespo-PiazueloJulia EckenbergerChloe E. HuseyinPeadar G. LawlorChristian ElendJaap A. WagenaarMarcus J. ClaessonAldert L. Zomer1Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands2WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands3School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland4SeqBiome Ltd., Cork, Ireland5Pig Development Department,Teagasc Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland6EW Nutrition Innovation GmbH & Co.KG, Cologne, Germany7Wageningen Bioveterinary Research, Lelystad, The NetherlandsTricia A. Van Laar
mSystems, Ahead of Print.
mSystems, Ahead of Print.
{"title":"The developing pig respiratory microbiome harbors strains antagonistic to common respiratory pathogens","authors":"Abel A. VlasblomBirgitta DuimShriram PatelRoosmarijn E. C. LuikenDaniel Crespo-PiazueloJulia EckenbergerChloe E. HuseyinPeadar G. LawlorChristian ElendJaap A. WagenaarMarcus J. ClaessonAldert L. Zomer1Faculty of Veterinary Medicine, Division of Infectious Diseases and Immunology, Utrecht University, Utrecht, The Netherlands2WHO Collaborating Centre for Reference and Research on Campylobacter and Antimicrobial Resistance from a One Health Perspective/WOAH Reference Laboratory for Campylobacteriosis, Utrecht, The Netherlands3School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland4SeqBiome Ltd., Cork, Ireland5Pig Development Department,Teagasc Animal & Grassland Research & Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland6EW Nutrition Innovation GmbH & Co.KG, Cologne, Germany7Wageningen Bioveterinary Research, Lelystad, The NetherlandsTricia A. Van Laar","doi":"10.1128/msystems.00626-24","DOIUrl":"https://doi.org/10.1128/msystems.00626-24","url":null,"abstract":"mSystems, Ahead of Print. <br/>","PeriodicalId":18819,"journal":{"name":"mSystems","volume":"17 1","pages":""},"PeriodicalIF":6.4,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142254207","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
Gut phageome in Mexican Americans: a population at high risk for metabolic dysfunction-associated steatotic liver disease and diabetes. 墨西哥裔美国人的肠道噬菌体组:代谢功能障碍相关性脂肪肝和糖尿病的高危人群。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-21 DOI: 10.1128/msystems.00434-24
Suet-Ying Kwan, Caroline M Sabotta, Lorenzo R Cruz, Matthew C Wong, Nadim J Ajami, Joseph B McCormick, Susan P Fisher-Hoch, Laura Beretta

Mexican Americans are disproportionally affected by metabolic dysfunction-associated steatotic liver disease (MASLD), which often co-occurs with diabetes. Despite extensive evidence on the causative role of the gut microbiome in MASLD, studies determining the involvement of the gut phageome are scarce. In this cross-sectional study, we characterized the gut phageome in Mexican Americans of South Texas by stool shotgun metagenomic sequencing of 340 subjects, concurrently screened for liver steatosis by transient elastography. Inter-individual variations in the phageome were associated with gender, country of birth, diabetes, and liver steatosis. The phage signatures for diabetes and liver steatosis were subsequently determined. Enrichment of Inoviridae was associated with both diabetes and liver steatosis. Diabetes was further associated with the enrichment of predominantly temperate Escherichia phages, some of which possessed virulence factors. Liver steatosis was associated with the depletion of Lactococcus phages r1t and BK5-T, and enrichment of the globally prevalent Crassvirales phages, including members of genus cluster IX (Burzaovirus coli, Burzaovirus faecalis) and VI (Kahnovirus oralis). The Lactococcus phages showed strong correlations and co-occurrence with Lactococcus lactis, while the Crassvirales phages, B. coli, B. faecalis, and UAG-readthrough crAss clade correlated and co-occurred with Prevotella copri. In conclusion, we identified the gut phageome signatures for two closely linked metabolic diseases with significant global burden. These phage signatures may have utility in risk modeling and disease prevention in this high-risk population, and identification of potential bacterial targets for phage therapy.IMPORTANCEPhages influence human health and disease by shaping the gut bacterial community. Using stool samples from a high-risk Mexican American population, we provide insights into the gut phageome changes associated with diabetes and liver steatosis, two closely linked metabolic diseases with significant global burden. Common to both diseases was an enrichment of Inoviridae, a group of phages that infect bacterial hosts chronically without lysis, allowing them to significantly influence bacterial growth, virulence, motility, biofilm formation, and horizontal gene transfer. Diabetes was additionally associated with the enrichment of Escherichia coli-infecting phages, some of which contained virulence factors. Liver steatosis was additionally associated with the depletion of Lactococcus lactis-infecting phages, and enrichment of Crassvirales phages, a group of virulent phages with high global prevalence and persistence across generations. These phageome signatures may have utility in risk modeling, as well as identify potential bacterial targets for phage therapy.

墨西哥裔美国人受代谢功能障碍相关性脂肪性肝病(MASLD)的影响不成比例,这种疾病通常与糖尿病并发。尽管有大量证据表明肠道微生物组在 MASLD 中的致病作用,但确定肠道噬菌体参与其中的研究却很少。在这项横断面研究中,我们通过对 340 名受试者进行粪便猎枪元基因组测序,确定了南得克萨斯州墨西哥裔美国人肠道噬菌体组的特征,并同时通过瞬时弹性成像技术筛查肝脏脂肪变性。噬菌体组的个体间差异与性别、出生国、糖尿病和肝脏脂肪变性有关。随后确定了糖尿病和肝脏脂肪变性的噬菌体特征。Inoviridae 的富集与糖尿病和肝脏脂肪变性有关。糖尿病还与主要是温带大肠杆菌噬菌体的富集有关,其中一些噬菌体具有毒力因子。肝脏脂肪变性与乳球菌噬菌体 r1t 和 BK5-T 的减少以及全球流行的 Crassvirales 噬菌体的富集有关,其中包括属群 IX(大肠伯沙病毒、粪伯沙病毒)和 VI(口腔卡诺病毒)的成员。乳球菌噬菌体与乳酸乳球菌有很强的相关性和共存性,而 Crassvirales 噬菌体、大肠杆菌、粪肠杆菌和 UAG-readthrough crAss 支系与 copri 普雷沃特氏菌有相关性和共存性。总之,我们发现了两种密切相关的代谢性疾病的肠道噬菌体组特征,这两种疾病在全球造成了巨大的负担。这些噬菌体特征可能对这一高危人群的风险建模和疾病预防有用,并能确定噬菌体疗法的潜在细菌靶标。我们利用高风险墨西哥裔美国人的粪便样本,深入研究了与糖尿病和肝脂肪变性这两种密切相关的代谢性疾病有关的肠道噬菌体组变化。这两种疾病的共同点是伊诺维病毒科(Inoviridae)噬菌体的富集,伊诺维病毒科是一组能长期感染细菌宿主而不溶解的噬菌体,它们能显著影响细菌的生长、毒力、活力、生物膜的形成和水平基因转移。糖尿病还与大肠杆菌感染噬菌体的富集有关,其中一些噬菌体含有毒力因子。肝脏脂肪变性还与乳酸乳球菌感染噬菌体的减少和Crassvirales噬菌体的富集有关。这些噬菌体组特征可用于风险建模,并确定噬菌体疗法的潜在细菌靶标。
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引用次数: 0
Minimal transcriptional regulation of horizontally transferred photosynthesis genes in phototrophic bacterium Gemmatimonas phototrophica. 光营养细菌 Gemmatimonas phototrophica 中水平转移的光合作用基因的最小转录调控。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-27 DOI: 10.1128/msystems.00706-24
Karel Kopejtka, Jürgen Tomasch, Sahana Shivaramu, Mohit Kumar Saini, David Kaftan, Michal Koblížek

The first phototrophic member of the bacterial phylum Gemmatimonadota, Gemmatimonas phototrophica AP64T, received all its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Here, we investigated how these acquired genes, which are tightly controlled by oxygen and light in the ancestor, are integrated into the regulatory system of its new host. G. phototrophica grew well under aerobic and semiaerobic conditions, with almost no difference in gene expression. Under aerobic conditions, the growth of G. phototrophica was optimal at 80 µmol photon m-2 s-1, while higher light intensities had an inhibitory effect. The transcriptome showed only a minimal response to the dark-light shift at optimal light intensity, while the exposure to a higher light intensity (200 µmol photon m-2 s-1) induced already stronger but still transient changes in gene expression. Interestingly, a singlet oxygen defense was not activated under any conditions tested. Our results indicate that G. phototrophica possesses neither the oxygen-dependent repression of photosynthesis genes known from purple bacteria nor the light-dependent repression described in aerobic anoxygenic phototrophs. Instead, G. phototrophica has evolved as a low-light species preferring reduced oxygen concentrations. Under these conditions, the bacterium can safely employ its photoheterotrophic metabolism without the need for complex regulatory mechanisms.

Importance: Horizontal gene transfer is one of the main mechanisms by which bacteria acquire new genes. However, it represents only the first step as the transferred genes have also to be functionally and regulatory integrated into the recipient's cellular machinery. Gemmatimonas phototrophica, a member of bacterial phylum Gemmatimonadota, acquired its photosynthesis genes via distant horizontal gene transfer from a purple bacterium. Thus, it represents a unique natural experiment, in which the entire package of photosynthesis genes was transplanted into a distant host. We show that G. phototrophica lacks the regulation of photosynthesis gene expressions in response to oxygen concentration and light intensity that are common in purple bacteria. This restricts its growth to low-light habitats with reduced oxygen. Understanding the regulation of horizontally transferred genes is important not only for microbial evolution but also for synthetic biology and the engineering of novel organisms, as these rely on the successful integration of foreign genes.

细菌门 Gemmatimonadota 的第一个光营养成员 Gemmatimonas phototrophica AP64T 通过远距离水平基因转移从一种紫色细菌获得了其所有的光合作用基因。在这里,我们研究了这些在祖先体内受氧和光严格控制的基因是如何整合到新宿主的调控系统中的。G. phototrophica 在有氧和半氧条件下生长良好,基因表达几乎没有差异。在有氧条件下,G. phototrophica 在 80 µmol photon m-2 s-1 的光照强度下生长最佳,而更高的光照强度会产生抑制作用。在最佳光照强度下,转录组对暗光转换的反应微乎其微,而在较高光照强度下(200 µmol photon m-2 s-1),基因表达的变化已经很强,但仍然是短暂的。有趣的是,在任何测试条件下,单线态氧防御都没有被激活。我们的研究结果表明,G. phototrophica 既不具有紫色细菌中已知的光合作用基因的氧依赖性抑制,也不具有需氧光养菌中描述的光依赖性抑制。相反,G. phototrophica 进化成了一种喜欢低氧浓度的低光照物种。在这些条件下,该细菌无需复杂的调控机制就能安全地进行光异养代谢:横向基因转移是细菌获得新基因的主要机制之一。然而,这仅仅是第一步,因为被转移的基因还必须在功能和调控上整合到接受者的细胞机制中。Gemmatimonas phototrophica 是细菌门 Gemmatimonadota 的一员,它的光合作用基因是通过紫色细菌的远距离水平基因转移获得的。因此,它代表了一个独特的自然实验,在这个实验中,光合作用的整套基因被移植到了一个遥远的宿主体内。我们发现 G. phototrophica 缺乏紫色细菌常见的光合作用基因表达对氧浓度和光照强度的调控。这限制了它在氧气减少的弱光环境中生长。了解横向转移基因的调控不仅对微生物进化很重要,而且对合成生物学和新型生物工程学也很重要,因为这些都依赖于外来基因的成功整合。
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引用次数: 0
Factors governing attachment of Rhizobium leguminosarum to legume roots at acid, neutral, and alkaline pHs. 豆科根瘤菌在酸性、中性和碱性 pH 值条件下附着在豆科植物根部的因素。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-21 DOI: 10.1128/msystems.00422-24
Jack D Parsons, Clare R Cocker, Alison K East, Rachel M Wheatley, Vinoy K Ramachandran, Farnusch Kaschani, Markus Kaiser, Philip S Poole

Rhizobial attachment to host legume roots is the first physical interaction of bacteria and plants in symbiotic nitrogen fixation. The pH-dependent primary attachment of Rhizobium leguminosarum biovar viciae 3841 to Pisum sativum (pea) roots was investigated by genome-wide insertion sequencing, luminescence-based attachment assays, and proteomic analysis. Under acid, neutral, or alkaline pH, a total of 115 genes are needed for primary attachment under one or more environmental pH, with 22 genes required for all. These include components of cell surfaces and membranes, together with enzymes that construct and modify them. Mechanisms of dealing with stress also play a part; however, exact requirements vary depending on environmental pH. RNASeq showed that knocking out the two transcriptional regulators required for attachment causes massive changes in the bacterial cell surface. Approximately half of the 54 proteins required for attachment at pH 7.0 have a role in the later stages of nodule formation. We found no evidence for a single rhicadhesin responsible for alkaline attachment, although sonicated cell surface fractions inhibited root attachment at alkaline pH. Our results demonstrate the complexity of primary root attachment and illustrate the diversity of mechanisms involved.

Importance: The first step by which bacteria interact with plant roots is by attachment. In this study, we use a combination of insertion sequencing and biochemical analysis to determine how bacteria attach to pea roots and how this is influenced by pH. We identify several key adhesins, which are molecules that enable bacteria to stick to roots. This includes a novel filamentous hemagglutinin which is needed at all pHs for attachment. Overall, 115 proteins are required for attachment at one or more pHs.

根瘤菌对寄主豆科植物根部的附着是细菌和植物在共生固氮过程中的第一次物理相互作用。通过全基因组插入测序、基于发光的附着试验和蛋白质组分析,研究了豆科根瘤菌(Rhizobium leguminosarum biovar viciae 3841)与豌豆(Pisum sativum)根的初级附着对 pH 值的依赖性。在酸性、中性或碱性 pH 值条件下,一种或多种环境 pH 值条件下的原生附着共需要 115 个基因,其中 22 个基因是全部需要的。这些基因包括细胞表面和细胞膜的组成成分,以及构建和改造细胞表面和细胞膜的酶。处理压力的机制也发挥了作用;不过,具体要求因环境 pH 值的不同而不同。RNASeq 研究表明,敲除附着所需的两个转录调节因子会导致细菌细胞表面发生巨大变化。在 pH 值为 7.0 时附着所需的 54 个蛋白质中,约有一半在结核形成的后期阶段发挥作用。尽管超声处理的细胞表面分馏物会抑制根在碱性 pH 值下的附着,但我们没有发现任何证据表明有单一的根瘤鞘蛋白负责碱性附着。我们的研究结果证明了原生根附着的复杂性,并说明了相关机制的多样性:重要意义:细菌与植物根系相互作用的第一步是附着。在这项研究中,我们结合插入测序和生化分析,确定了细菌如何附着在豌豆根上,以及这种附着如何受到 pH 值的影响。我们发现了几种关键的粘附素,它们是使细菌能够粘附到根部的分子。其中包括一种新型丝状血凝素,它在所有 pH 值下都需要进行附着。总体而言,有 115 种蛋白质需要在一种或多种 pH 值条件下进行附着。
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引用次数: 0
Pangenomic landscapes shape performances of a synthetic genetic circuit across Stutzerimonas species. 庞基因组景观决定了合成基因回路在不同Stutzerimonas物种中的表现。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-21 DOI: 10.1128/msystems.00849-24
Dennis Tin Chat Chan, Hans C Bernstein

Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the "chassis-effect" or "context-dependency". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related Stutzerimonas hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.IMPORTANCEContemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as Escherichia coli serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function. Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.

由于每个宿主独特的细胞环境背景,将相同的基因回路植入不同物种通常会导致性能上的巨大差异,这种现象被称为 "底盘效应 "或 "环境依赖性"。更好地了解基因组和生理环境是如何支撑底盘效应的,将有助于改进不同微生物的生物设计策略。在这里,我们将基于泛基因组学的基因表达分析与工程基因变频装置性能的定量测量相结合,揭示了基因组结构和功能与六种密切相关的Stutzerimonas宿主所观察到的底盘效应之间的关系。我们的研究结果表明,基因组结构是我们选择的非模式细菌宿主对工程化装置产生不同反应的基础。具体来说,我们发现核心基因组(所有宿主共有的基因簇)的差异表达是导致所观察到的基因装置性能差异的主要原因,而来自各自附属基因组的特异基因并不显著。一项数据驱动的调查显示,参与反硝化的基因和跨膜转运蛋白的成分是宿主之间对基因装置反应差异最大的基因簇。我们的研究结果表明,底盘效应可以沿着最保守的基因组编码功能之间的差异进行追踪,这些差异在密切相关的物种之间创造了独特的生物设计空间。大肠杆菌等模式生物因其可操作性而成为具有吸引力的宿主,但并不一定能提供优化性能的理想环境。随着越来越多的新型微生物被驯化用作生物技术平台,合成生物学家必须探索底盘设计空间,以优化他们的系统,实现合成生物学的承诺。因此,随着生物设计领域的发展,底盘效应的后果只会变得更加重要。在我们的工作中,我们证明了基因装置的性能高度依赖于其运行的宿主环境,从而推广了底盘可被视为调整电路功能的设计变量这一概念。重要的是,我们的研究结果揭示了底盘效应可以沿着基因组结构的相似性进行追踪,特别是共享核心基因组。我们的研究倡导探索底盘设计空间,并为合成生物学家提供了更有效探索底盘设计空间的知识,使下一代广泛的合成生物学向前迈进了一步。
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引用次数: 0
Fungal elemental profiling unleashed through rapid laser-induced breakdown spectroscopy (LIBS). 通过快速激光诱导击穿光谱(LIBS)进行真菌元素分析。
IF 5 2区 生物学 Q1 MICROBIOLOGY Pub Date : 2024-09-17 Epub Date: 2024-08-27 DOI: 10.1128/msystems.00919-24
Tomás A Rush, Ann M Wymore, Miguel Rodríguez, Sara Jawdy, Rytas J Vilgalys, Madhavi Z Martin, Hunter B Andrews

Elemental profiling of fungal species as a phenotyping tool is an understudied topic and is typically performed to examine plant tissue or non-biological materials. Traditional analytical techniques such as inductively coupled plasma-optical emission spectroscopy (ICP-OES) and inductively coupled plasma-mass spectrometry (ICP-MS) have been used to identify elemental profiles of fungi; however, these techniques can be cumbersome due to the difficulty of preparing samples. Additionally, the instruments used for these techniques can be expensive to procure and operate. Laser-induced breakdown spectroscopy (LIBS) is an alternative elemental analytical technique-one that is sensitive across the periodic table, easy to use on various sample types, and is cost-effective in both procurement and operation. LIBS has not been used on axenic filamentous fungal isolates grown in substrate media. In this work, as a proof of concept, we used LIBS on two genetically distinct fungal species grown on a nutrient-rich and nutrient-poor substrate media to determine whether robust elemental profiles can be detected and whether differences between the fungal isolates can be identified. Our results demonstrate a distinct correlation between fungal species and their elemental profile, regardless of the substrate media, as the same strains shared a similar uptake of carbon, zinc, phosphorus, manganese, and magnesium, which could play a vital role in their survival and propagation. Independently, each fungal species exhibited a unique elemental profile. This work demonstrates a unique and valuable approach to rapidly phenotype fungi through optical spectroscopy, and this approach can be critical in understanding these fungi's behavior and interactions with the environment.

Importance: Historically, ionomics, the elemental profiling of an organism or materials, has been used to understand the elemental composition in waste materials to identify and recycle heavy metals or rare earth elements, identify the soil composition in space exploration on the moon or Mars, or understand human disorders or disease. To our knowledge, ionomic profiling of microbes, particularly fungi, has not been investigated to answer applied and fundamental biological questions. The reason is that current ionomic analytical techniques can be laborious in sample preparation, fail to measure all potential elements accurately, are cost-prohibitive, or provide inconsistent results across replications. In our previous efforts, we explored whether laser-induced breakdown spectroscopy (LIBS) could be used in determining the elemental profiles of poplar tissue, which was successful. In this proof-of-concept endeavor, we undertook a transdisciplinary effort between applied and fundamental mycology and elemental analytical techniques to address the biological question of how LIBS can used for fungi grown axenically in a nutrient-rich and nutrient-poor environment.

作为一种表型工具,真菌物种的元素分析是一个研究不足的课题,通常是对植物组织或非生物材料进行检测。传统的分析技术,如电感耦合等离子体-光学发射光谱分析法(ICP-OES)和电感耦合等离子体-质谱分析法(ICP-MS),已被用于鉴定真菌的元素谱;然而,由于制备样品的困难,这些技术可能比较麻烦。此外,这些技术所使用的仪器采购和操作成本也很高。激光诱导击穿光谱(LIBS)是一种可供选择的元素分析技术--它对整个元素周期表都很敏感,易于在各种类型的样品上使用,而且在采购和操作方面都具有成本效益。LIBS 尚未用于在基质培养基中生长的轴丝真菌分离物。在这项工作中,作为概念验证,我们对生长在富营养和贫营养基质培养基上的两种基因不同的真菌物种使用了 LIBS,以确定是否能检测到稳健的元素谱,以及是否能识别真菌分离物之间的差异。我们的研究结果表明,无论基质介质如何,真菌种类与其元素特征之间都存在明显的相关性,因为相同的菌株对碳、锌、磷、锰和镁的吸收量相似,这可能对它们的生存和繁殖起着至关重要的作用。每种真菌都表现出独特的元素特征。这项工作展示了一种通过光学光谱快速对真菌进行表型的独特而有价值的方法,这种方法对于了解这些真菌的行为以及与环境的相互作用至关重要:从历史上看,离子组学,即对生物体或材料进行元素分析,一直被用于了解废料中的元素组成,以确定和回收重金属或稀土元素,确定月球或火星太空探索中的土壤成分,或了解人类失调或疾病。据我们所知,微生物(尤其是真菌)的离子组学分析还没有被研究用于回答应用和基础生物学问题。究其原因,目前的离子组分析技术在样品制备过程中可能很费力,无法准确测量所有潜在元素,成本高昂,或在不同重复中提供不一致的结果。在之前的工作中,我们探索了激光诱导击穿光谱(LIBS)是否可用于确定杨树组织的元素特征,并取得了成功。在这次概念验证工作中,我们在应用和基础真菌学以及元素分析技术之间进行了跨学科合作,以解决如何利用激光诱导击穿光谱(LIBS)测定在营养丰富和营养缺乏环境中轴向生长的真菌的生物学问题。
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