The Laboratory for Microbiome Sciences has been engaged in the study of 50dsDNA phagessDNA phage72%1.5%Microbiome sampleVirus-like particlesViromeDNAAssembled genomesVLP enrichmentViral DNA extractionMultiple displacement amplification(MDA)Long-read metagenomicsSplit Amplified Chimeric Read Algorithm(SACRA)AssemblyCompleteShort-read metagenomicsAssemblyFragmentedthe complex interactions between symbiotic microbial ecosystems (com-posed of bacteria, viruses and fungi) and their hosts. Through the development of new experimental and informatics-based technologies using state-of-the-art sequencers, we aim to comprehensively understand and eventually control these symbiotic microbial ecosystems by clarifying not only the microbiome structure variation among individuals but also the time-series dynamics.Currently, our team has published 15 papers in FY2021. In one represen-tative paper, we have developed a novel long-read metagenomic method to analyze the viral community (virome) in the human gut (DNA Res. 2021 Oct 11;28(6):dsab019.). Our method amplifies the very low amount of double and single-strand viral genomic DNA in a human fecal sample by multiple displace-ment amplification (MDA) to obtain sufficient DNA for long-read sequencing. A novel bioinformatic method, SACRA, developed in our lab can efficiently correct the artificial chimeric reads generated by MDA to non-chimeric reads. De novo assembly using SACRA-treated long reads reconstructs high-quality phage genomes, which are often fragmented in conventional short-read data because of the community’s genomic complexity. This technology reveals the previously undetectable characteristics of the human gut virome and contrib-utes to clarifying the role of viruses in the human gut microbiome.We are also constructing a high-quality genomic database by independently compiling the microbial chromosomes, plasmids, and phages from human gut long-read metagenomics of the Japanese cohort. This database is composed of various novel genetic elements with high completeness and is expected to pro-vide a foundation for diversified human gut microbiome.Figure: SACRA-coupled long-read metagenomics for virome analysisOur method extracts virus-like particles (mainly double and single-strand DNA phages) from human fecal samples and obtains the virome DNA. Then the low-biomass virome DNA is amplified by multiple displace-ment amplification (MDA) to obtain sufficient DNA for sequencing. Conventionally, the MDA-treated virome DNA is sequenced by a short-read sequencer, but subse-quent assembly generates highly fragmented genomes. Our method can reconstruct complete phage genomes using long reads preprocessed by the novel bioinformat-ics tool SACRA for reducing the chimeric reads generated by MDA.Recent Major PublicationsFuruhashi H, Takayasu L, Isshi K, Hara Y, Ono S, Kato M, Sumiyama K, Suda W. Effect of storage temperature and flash-freezing on salivary microbiota profiles based on 16S rRNA-targeted sequencing. Eur J Oral Sci 20, e12852 (2022)Kiguchi Y, Nishijima S, Kumar N, Hattori M, Suda W. Long-read metagenomics of multiple displacement amplified DNA of low-biomass human gut phageomes by SACRA pre-processing chimeric reads. DNA Res 28, dsab019 (2021)Cariño R 3rd, Takayasu L, Suda W, Masuoka H, Hirayama K, Konishi S, Umezaki M. The search for aliens within us: a review of evidence and theory regarding the foetal microbiome. Crit Rev Microbiol 17, 1-13 (2021)Invited presentationsSuda W. “Research of the Human Gut and Oral Micro-biome”, OMC Gastroenterology Conference (Online) November 2021Suda W. “Trends and Examples of Human Microbiome Research”, Diabetes Web Lecture Organized by Nippon Boehringer Ingelheim Co., Ltd (Online) October 2021Suda W. “Trends and Applications of Microbiome Analy-sis” Educational Lecture, The 120th Annual Meeting of the Japanese Dermatological Association (Yokohama, Japan/Online) June 2021Laboratory for Microbiome SciencesTeam Leader: Hiroshi Ohno
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