Conservation of genomic information in multiple displacement amplified low-quantity metagenomic material from marine invertebrates. MDA Metagenomes of Marine Invertebrates

Marine invertebrates and their microbiomes have been a rich source of bioactive compounds and interesting genomic features. However, factors such as which species and tissue are targeted, options for sample collection, and methods for sample preparations might cause the obtainable amount of DNA to be too low for direct sequencing. Multiple displacement amplification (MDA) is the most used method for whole genome amplification (WGA) in such cases. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. Here, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA-products from marine invertebrate microbiomes collected from Arctic and sub-Arctic areas. Bacteria-sized cells were separated from their marine invertebrate hosts, subjected to MDA, and the MDA-products sequenced by Illumina sequencing. A set of three reference strains were cultured and treated the same way. Despite MDA making it challenging to achieve high quality assemblies, the resulting genomic sequences gave useful information on the taxonomical profile and the biosynthetic potential of the MDA-products and made it possible to select samples were further efforts to achieve high quality metagenomes were likely to result in the discovery of interesting BGCs.

海洋无脊椎动物及其微生物组一直是生物活性化合物与具有研究价值的基因组特征的丰富来源。然而，诸如目标物种与组织、样本采集方案以及样本制备方法等因素，可能导致可获取的DNA总量过低，无法直接进行测序。多重置换扩增（Multiple displacement amplification, MDA）是此类场景中应用最为广泛的全基因组扩增（Whole genome amplification, WGA）方法。但多重置换扩增存在已知的局限性，会影响所得基因组与宏基因组的质量。本研究针对从北极及亚北极区域采集的海洋无脊椎动物微生物组的多重置换扩增产物，评估了其生物合成基因簇（Biosynthetic gene clusters, BGCs）与酶的保守性。研究人员从海洋无脊椎动物宿主中分离出细菌尺寸的细胞，进行多重置换扩增后，采用Illumina测序技术对扩增产物进行测序。同时设置三株参考菌株，对其进行培养并施以相同的处理流程。尽管多重置换扩增难以获得高质量的基因组组装结果，但所得基因组序列仍为扩增产物的分类学特征与生物合成潜力提供了有效信息，并可据此筛选样本，使得后续为获取高质量宏基因组而开展的研究更有可能发现具有研究价值的生物合成基因簇。