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在干草堆里找针：直接从自然环境中对复杂微生物基因组进行非培养扩增。

Turning the needle into the haystack: Culture-independent amplification of complex microbial genomes directly from their native environment.

机构信息

Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

Department of Pediatrics, Children's Hospital of Philadelphia, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America.

出版信息

PLoS Pathog. 2024 Sep 12;20(9):e1012418. doi: 10.1371/journal.ppat.1012418. eCollection 2024 Sep.

DOI:10.1371/journal.ppat.1012418
PMID:39264872
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11392400/
Abstract

High-throughput sequencing (HTS) has revolutionized microbiology, but many microbes exist at low abundance in their natural environment and/or are difficult, if not impossible, to culture in the laboratory. This makes it challenging to use HTS to study the genomes of many important microbes and pathogens. In this review, we discuss the development and application of selective whole genome amplification (SWGA) to allow whole or partial genomes to be sequenced for low abundance microbes directly from complex biological samples. We highlight ways in which genomic data generated by SWGA have been used to elucidate the population dynamics of important human pathogens and monitor development of antimicrobial resistance and the emergence of potential outbreaks. We also describe the limitations of this method and propose some potential innovations that could be used to improve the quality of SWGA and lower the barriers to using this method across a wider range of infectious pathogens.

摘要

高通量测序 (HTS) 彻底改变了微生物学，但许多微生物在其自然环境中丰度较低，或者在实验室中难以培养，如果不是不可能的话。这使得使用 HTS 研究许多重要微生物和病原体的基因组具有挑战性。在这篇综述中，我们讨论了选择性全基因组扩增 (SWGA) 的发展和应用，该方法允许对低丰度微生物的整个或部分基因组进行测序，而无需对复杂的生物样本进行培养。我们强调了 SWGA 生成的基因组数据在阐明重要人类病原体的种群动态、监测抗生素耐药性的发展以及潜在爆发的出现方面的应用。我们还描述了该方法的局限性，并提出了一些潜在的创新方法，可用于提高 SWGA 的质量，并降低在更广泛的传染病原体中使用该方法的障碍。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/a9a2b1637449/ppat.1012418.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/c8c8021c49f9/ppat.1012418.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/70620b595e5a/ppat.1012418.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/046418e14117/ppat.1012418.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/a9a2b1637449/ppat.1012418.g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/c8c8021c49f9/ppat.1012418.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/70620b595e5a/ppat.1012418.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/046418e14117/ppat.1012418.g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/6bea/11392400/a9a2b1637449/ppat.1012418.g004.jpg

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