Conservation of genomic information in multiple displacement amplified low-quantity metagenomic material from 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.