Abstract
Since the intestinal microbiota has a significant impact on the physiological state of the host, the development of technologies to control it is an urgent task. It is also thought that there are twice as many phages as bacteria in the intestine, and although the relationship between diseases and the intestinal phage flora is being reported, the overall structure of the intestinal phage flora and its relationship with diseases are still largely unknown. In this study, we performed metagenomic analysis of the intestinal phage flora of healthy Japanese people and multiple sclerosis (MS) patients to construct full-length genomes and deepen our understanding of the overall structure, and to explore the relationship between the intestinal phage flora and diseases and the possibility of controlling their pathology.
Feces were collected from a total of 90 volunteers, including those with relapsing-remitting MS, progressive MS, and healthy individuals, and DNA and RNA were extracted, followed by shotgun metagenomics and RNA sequencing using short- and long-type sequencers. The resulting reads were used for assembly, quality checks, and high-quality contigs were obtained. The high-quality contigs were classified using various tools to obtain full-length or nearly full-length phage genomes. The obtained phage genomes were subjected to gene function analysis and host estimation to identify the characteristics of the phages and to confirm the relationship between gene expression levels and diseases.
By assembling short and long reads, 6,185 nearly full-length phage genomes were obtained. When the obtained phage genomes were subjected to a homology search in existing phage genome databases, more than half were phages with novel genome sequences that had not been reported before. As a result of performing a pipeline process for host estimation, it was possible to estimate the hosts for approximately half of the phages. By using these phages as a reference, we analyzed the intestinal phage flora of MS patients and discovered phages and phage-derived functions (coenzyme B12 biosynthesis) that were significantly decreased by the disease. We also discovered active lysogenic phages that activate some pathogenic intestinal bacterial species by treating them with mitomycin. We are also investigating the control of pathogenic bacteria using these phages.
