Improved metagenome assemblies through selective enrichment of bacterial genomic DNA from eukaryotic host genomic DNA using ATAC-seq

• Published in: Frontiers in microbiology 2024-02, Vol.15, p.1352378-1352378
• Main Authors: Cantin, Lindsey J, Dunning Hotopp, Julie C, Foster, Jeremy M
• Format: Article
• Language: English
• Subjects: ATAC-seq; bacterial symbiont; epigenetics; filariasis; genome assembly; Microbiology; Wolbachia
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2024.1352378

Genomics can be used to study the complex relationships between hosts and their microbiota. Many bacteria cannot be cultured in the laboratory, making it difficult to obtain adequate amounts of bacterial DNA and to limit host DNA contamination for the construction of metagenome-assembled genomes (MAGs). For example, is a genus of exclusively obligate intracellular bacteria that live in a wide range of arthropods and some nematodes. While endosymbionts are frequently described as facultative reproductive parasites in arthropods, the bacteria are obligate mutualistic endosymbionts of filarial worms. Here, we achieve 50-fold enrichment of bacterial sequences using ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) with nematodes, containing ( Bm). ATAC-seq uses the Tn5 transposase to cut and attach Illumina sequencing adapters to accessible DNA lacking histones, typically thought to be open chromatin. Bacterial and mitochondrial DNA in the lysates are also cut preferentially since they lack histones, leading to the enrichment of these sequences. The benefits of this include minimal tissue input (