Nanopore Long Reads: Farewell to Blind Spots in Microbiome Research
时长:27:57 分会场:2019中国肠道大会 - 新技术大会
希望组&未来组 首席技术官
DNA inversions mediate phase variable antibiotic resistance and interhost adaptation in gut bacteria
As an actionable target for diagnostic tools and therapeutic interventions, the human microbiome has emerged as a critically important research topic. The rise of the microbiome field has been propelled by high-throughput sequencing. However, the bioinformatic tools for analyzing microbiome data are still evolving and formidable challenges remain in establishing the foundation of taxonomy, dynamics and function of the human microbiome. Here, I developed the PhaseFinder algorithm to quantify DNA inversion-mediated phase variation. A systematic search of 54,875 bacterial genomes identified 4,686 intergenic invertible DNA regions (invertons) revealing an enrichment in host-associated bacteria. We found invertons containing promoters regulating antibiotic resistance genes that shift to the ON orientation following antibiotic treatment in human metagenomic data and in vitro, thereby mitigating the cost of antibiotic resistance. We observed that the orientations of some invertons diverge after fecal microbiota transplant, potentially due to individual-specific selective forces.
江晓芳 时长:22:18
化学工具的发展可以为肠道菌群研究提供新的研究角度和工具,报告中将介 绍我们近期利用基于 D-型氨基酸的代谢探针,采用序贯标记的方式(sequential tagging with D-amino acid-based metabolic probes, STAMP)实现了粪菌移植过程中植入菌的成像追踪与在受体小鼠体内存活情况的评估,解决了粪菌移植中潜在的发挥治疗效用的细菌种类鉴别这一难题,为深入理解这一极为复杂但又潜力巨大的微生物疗法提供了研究工具, 也为这一疗法的步骤优化与标准化提供了研究方法。此外,还将介绍我们最近在体内菌群实时观察成像方面的工作进展。通过使用带有炔基的 D-型氨基酸探针,在体内代谢标记供体肠道菌群之后,再配合使用带有叠氮基团的红外 II 区荧光染料在体外进行点击化学反应,将荧光基团偶联到菌群表面。将这一菌群植入受体小鼠之后,目前已可以实现小鼠体内菌群的活体实时成像观察,并将成像方法拓展到了各类常见的致病菌与共生菌菌株的在体成像观察中。
王炜 时长:21:15
Background and Aims: The loss of long-range sequence contiguity in the process of NGS sequencing is an obstacle to understanding the structure and function of genomes and metagenomes. This obstacle negatively affects both clinical research efforts and virtually all microbiome-centric projects as much genetic information cannot be reconstructed from complex mixed microbial communities without culturing the constituent microbes. Methods and Results: The chromosome conformation capture method, Hi-C, restores chromosome-scale contiguity to large genome assemblies and enables the deconvolution of numerous genomes from mixed samples such as complex microbial communities. Hi-C captures genomic proximity interactions through in vivo crosslinking, followed by proximity-ligation and sequencing. Since the crosslinks occur inside intact cells, any two loci that interact by Hi-C must have originated in the same cell, and this data can be used to deconvolute high quality genomes directly from mixed populations. We have developed a metagenomic discovery platform that exploits Hi-C proximity-ligation data and have applied it to a number of diverse sample types. Our ProxiMeta Hi-C extracts large numbers of genomes directly from microbiome samples without culturing, which can also associate plasmids and phage with hosts and separate strains without culturing. Conclusions: We will discuss the application of Hi-C data to a number of diverse microbiome samples. For example, we have been able to discover hundreds of novel strains and species from fecal and infected samples, as well as identify novel plasmid/phage host interactions.We have been able to identify the host for a number of AMR genes within novel species, underscoring the value of proximity-ligation data to microbiome research.
Ivan Liachko 时长:20:08