Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients.
Hi-C Metagenomics in the ICU: Exploring Clinically Relevant Features of Gut Microbiome in Chronically Critically Ill Patients.
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DOI：
10.3389/fmicb.2021.770323
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发表时间：
2021
影响因子：
5.2
通讯作者：
Tyakht A
中科院分区：
文献类型：
--
作者：
Ivanova V;Chernevskaya E;Vasiluev P;Ivanov A;Tolstoganov I;Shafranskaya D;Ulyantsev V;Korobeynikov A;Razin SV;Beloborodova N;Ulianov SV;Tyakht A
重症患者的肠道微生物组显示出严重的生态失调。最脆弱的是慢性危重病（CCI）患者的亚组-那些长期依赖重症监护室支持系统的患者。重要的是要调查他们的微生物组作为一个潜在的水库的机会性分类群引起合并感染和发病因素。我们通过将“鸟枪法”宏基因组学与染色体构象捕获（Hi-C）相结合来探索CCI患者中微生物组组成的动态。在1-2周间隔内，在2个时间点收集2例具有不同结局的重度脑损伤患者的粪便样本。使用新的hicSPAdes方法（沿着用于比较的bin 3c方法）基于Hi-C数据以及独立于Hi-C使用MetaBAT 2重建宏基因组组装的基因组（MAG）。使用一种新的组装图为基础的方法来获得样品的电阻。使用基于Hi-C的网络分析了细菌与抗生素抗性基因、质粒和病毒的联系。肠道群落结构中富含机会微生物。在重建的MAG的数量、完整性和污染方面，使用hicSPAdes的分箱上级传统的基于WGS的分箱以及bin 3c。以肺炎克雷伯菌为例，我们展示了染色体构象捕获如何有助于临床重要病原体的比较基因组分析。从组装图到基因含量，耐药基因组与抗生素治疗存在多种关联。Hi-C网络的分析表明存在多个“宿主-质粒”和“宿主-噬菌体”链接。Hi-C宏基因组学是研究临床微生物组样本的一种有前途的技术。与传统的宏基因组学相比，它提供了一个群落组成概况，其中细菌基因含量和移动的遗传元件的细节增加。Hi-C分箱涵盖MAG质粒内容物的能力有助于对临床相关机会致病菌的毒力和耐药性动力学进行宏基因组学评价。这些发现将有助于确定开发具有成本效益和快速测试的目标，以评估微生物组相关的健康风险。
Gut microbiome in critically ill patients shows profound dysbiosis. The most vulnerable is the subgroup of chronically critically ill (CCI) patients – those suffering from long-term dependence on support systems in intensive care units. It is important to investigate their microbiome as a potential reservoir of opportunistic taxa causing co-infections and a morbidity factor. We explored dynamics of microbiome composition in the CCI patients by combining “shotgun” metagenomics with chromosome conformation capture (Hi-C). Stool samples were collected at 2 time points from 2 patients with severe brain injury with different outcomes within a 1–2-week interval. The metagenome-assembled genomes (MAGs) were reconstructed based on the Hi-C data using a novel hicSPAdes method (along with the bin3c method for comparison), as well as independently of the Hi-C using MetaBAT2. The resistomes of the samples were derived using a novel assembly graph-based approach. Links of bacteria to antibiotic resistance genes, plasmids and viruses were analyzed using Hi-C-based networks. The gut community structure was enriched in opportunistic microorganisms. The binning using hicSPAdes was superior to the conventional WGS-based binning as well as to the bin3c in terms of the number, completeness and contamination of the reconstructed MAGs. Using Klebsiella pneumoniae as an example, we showed how chromosome conformation capture can aid comparative genomic analysis of clinically important pathogens. Diverse associations of resistome with antimicrobial therapy from the level of assembly graphs to gene content were discovered. Analysis of Hi-C networks suggested multiple “host-plasmid” and “host-phage” links. Hi-C metagenomics is a promising technique for investigating clinical microbiome samples. It provides a community composition profile with increased details on bacterial gene content and mobile genetic elements compared to conventional metagenomics. The ability of Hi-C binning to encompass the MAG’s plasmid content facilitates metagenomic evaluation of virulence and drug resistance dynamics in clinically relevant opportunistic pathogens. These findings will help to identify the targets for developing cost-effective and rapid tests for assessing microbiome-related health risks.
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影响因子：
3.2
作者：
ARTHUR, M;MOLINAS, C;COURVALIN, P
通讯作者：
COURVALIN, P
影响因子：
14.9
作者：
Krawczyk PS;Lipinski L;Dziembowski A
通讯作者：
Dziembowski A
影响因子：
5.7
作者：
Dufresne K;Saulnier-Bellemare J;Daigle F
通讯作者：
Daigle F
影响因子：
5.9
作者：
Klimenko NS;Tyakht AV;Popenko AS;Vasiliev AS;Altukhov IA;Ischenko DS;Shashkova TI;Efimova DA;Nikogosov DA;Osipenko DA;Musienko SV;Selezneva KS;Baranova A;Kurilshikov AM;Toshchakov SM;Korzhenkov AA;Samarov NI;Shevchenko MA;Tepliuk AV;Alexeev DG
通讯作者：
Alexeev DG
DOI：
10.1093/bioinformatics/bty630
发表时间：
2019-02-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Gourlé H;Karlsson-Lindsjö O;Hayer J;Bongcam-Rudloff E
通讯作者：
Bongcam-Rudloff E