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Human Genome Center

Division of Metagenome Medicine
メタゲノム医学分野

Project Professor
Satoshi Uematsu, M.D., Ph.D.
Project Associate Professor Kosuke Fujimoto, M.D., Ph.D.

特任教授
特任准教授

博士（医学）
博士（医学）

植藤松
本康

智介

Abnormal compositions of intestinal microbiota have been reported to beassociated with various diseases. We analyze intestinal bacteriome and virome invarious diseases and search for “pathobiont” that causes the diseases. By making
use of bioinformatics, we are constructing an analysis pipeline for intestinal
microbiome, conducting comprehensive metagenomic analysis, and developing
phage therapy for the specific control of pathobionts.

1.  Analysis of intestinal microbiota in diseases.
Kosuke Fujimoto1, Seiya Imoto2 and Satoshi Uematsu1
1
Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The
University of Tokyo. 2Division of Health Medical Inteligence, Human Genome Center, The Institute ofMedical Science, The University of Tokyo. 3Divisionof Metagenome Medicine, Human Genome Center,
The Institute of Medical Science, The University ofTokyo.
In recent years, intestinal dysbiosis has been detected in a variety of diseases. It has become clear thatdysbiosis is involved in the pathogenesis of these diseases. We collected fecal samples from 10 Crohn’s disease patients in remission and performed metagenomic analysis. Disease-specific defective bacteria andgene pathways have been identified. We identified
metabolites that may accumulate in the intestine as aresult of changes in intestinal bacteria. It has beensuggested that this metabolite may produce substances that induce inflammation and contribute to the induction of enteritis. Graft-versus-host disease is a serious side effect after bone marrow transplantation inleukemia patients. We are collecting fecal samples
over time and performing metagenomic analysis inpatients with bone marrow transplantation. We haveidentified Enterococcus faecalis that increase in the gut
after bone marrow transplantation. Interestingly, E.
faecalis isolated from the patients are cytolysin positive virulent strain and may increase the risk ofGVHD. Functional analysis of E. faecalis is currently
underway.
2.  Development of a microbiome digital twin to
predict disease states based on metagenome
analysis of intestinal microflora
Kosuke Fujimoto1, Seiya Imoto2 and Satoshi Uematsu11Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The
University of Tokyo. 2Division of Health Medical Inteligence, Human Genome Center, The Institute ofMedical Science, The University of Tokyo. 3Divisionof Metagenome Medicine, Human Genome Center,The Institute of Medical Science, The University ofTokyo.
We are developing a digital twin that predicts disease states using metagenomic data of the intestinal
microbiota and gene pathway analysis data as teaching data. For this purpose, we collected fecal samples
from 10 Crohn’s disease patients and 18 Parkinson’s

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disease patients and performed metagenomic analysis. Currently, under collaboration with Fujitsu, weare comparing these data with metagenomic data of
100 healthy subjects and performing machine learning and deep learning.
3.  Development of phage therapy
Kosuke Fujimoto1, Seiya Imoto2 and Satoshi Uematsu1
1Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, TheUniversity of Tokyo. 2Division of Health Medical Inteligence, Human Genome Center, The Institute ofMedical Science, The University of Tokyo. 3Divisionof Metagenome Medicine, Human Genome Center,
The Institute of Medical Science, The University ofTokyo.
Our intestinal tract carries a lot of bacteria in thelumen as the resident microorganism. In addition toresident bacteria, viruses are also present in our intestinal tract, most of which are bacteriophages. However, it is still unclear what kind of bacteriophage exist
in our intestinal tract, and what kind of bacteria they
infect with. As one of the reasons, isolation of viralnucleic acids and preparation of libraries have notbeen established. Since conserved sequence such as
16s rRNA gene do not exist in virus, whole genome
analysis is necessary. Even if comprehensive wholegenome analysis of intestinal viruses were performed,
most of the sequence fragments couldn’t be classified
by homology search due to the insufficient public databases. Thus, virome analysis is relatively difficultcompared with bacteiome analysis and this situation
is expressed by the word “vral dark matter”. We havedeveloped the isolation method of intestinal viruses.
We also have generated analysis pipeline of metagenome analysis of viral genome and the method to analyze host-parasite association identified based on theshotgun sequencing data of the bacterial flora and viral plexus. We are compiling an comprehensive catalog of enzymes derived from phage infecting Acinetobacter baumannii for the purpose of developing
next-generation phage therapies against Gram-negative bacteria. We are also developing a platform forthe creation of artificial phage capable of killing Escherichia coli.
4.  Development of next-generation mucosal vaccine against infectious diseases
Kosuke Fujimoto1, Satoshi Uematsu1
1
Division of Metagenome Medicine, Human Genome Center, The Institute of Medical Science, The
University of Tokyo.
A next-generation vaccine strategy capable of inducing both systemic and mucosal immunity is await-ed. We showed that intramuscular vaccination with a
combination of CpG oligodeoxynucleotides and curdlan as adjuvants systemically induced antigen-specific IgA and IgG production in mice. After priming,
markedly high titers and long-lasting antigen-specificIgA and helper T-cell responses including Th1 andTh17 responses in the mucosa were acquired by antigen boosting of the target organs. This immunization
effectively regulated Streptococcus pneumoniae infection in mice. The patent of this new vaccine strategy
was granted in 2019 in Japan, in 2020 in US and in
2021 in Europe. We are currently conducting monkey
experiments for formulation in human on the basis ofcollaboration with Mitsubishi Tanabe Pharmaceuticalcompany by using PspA, a universal Ag of S. pneumoniae. Although vaccination is recommended for protection against invasive pneumococcal disease, thefrequency of pneumococcal pneumonia is still highworldwide. In fact, no vaccines are effective for all
pneumococcal serotypes. Fusion pneumococcal surface protein A (PspA) has been shown to induce abroad range of cross-reactivity with clinical isolates
and afford cross-protection against pneumococcal
challenge in mice. Furthermore, we developed primeboost-type mucosal vaccines that induce both antigen-specific IgG in serum and antigen-specific IgA intargeted mucosal organs in previous studies. We investigated whether our prime-boost-type immunization with a fusion PspA was effective against pneumococcal infection in mice and cynomolgus macaques.
C57BL/6 mice were intramuscularly injected with fusion PspA combined with CpG oligodeoxynucleotides and/or curdlan. Six weeks later, PspA was administered intranasally. Blood and bronchoalveolarlavage fluid were collected and antigen-specific IgG
and IgA titers were measured. Some mice were given
intranasal Streptococcus pneumoniae and the severity of infection was analyzed. Macaques were intramuscularly injected with fusion PspA combined withCpG oligodeoxynucleotides and/or curdlan at week 0
and week 4. Then, 13 or 41 weeks later, PspA was administered intratracheally. Blood and bronchoalveolar lavage fluid were collected and antigen-specificIgG and IgA titers were measured. Some macaques
were intranasally administered S. pneumoniae andanalyzed for the severity of pneumonia. Serum samples from mice and macaques injected with antigens
in combination with CpG oligodeoxynucleotides and/or curdlan contained antigen-specific IgG. Bronchialsamples contained antigen-specific IgA after the fusion PspA boosting. This immunization regimen effectively prevented S. pneumoniae infection. Primeboost-type immunization with a fusion PspA
prevented S. pneumoniae infection in mice and macaques.

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Publications
Takaori A, Hashimoto D, Ikeura T, Ito T, Nakamaru
K, Masuda M, Nakayama S, Yamaki S, YamamotoT, Fujimoto K, Matsuo Y, Akagawa S, Ishida M,
Yamaguchi K, Imoto S, Hirota K, Uematsu S, Satoi
S, Sekimoto M, Naganuma M. Impact of neoadjuvant therapy on gut microbiome in patients withresectable/borderline resectable pancreatic ductal
adenocarcinoma. Pancreatology. 23(4):367-376,2023.
Zhang YZ, Liu Y, Bai Z, Fujimoto K, Uematsu S, Imoto
S. Zero-shot-capable identification of phage-hostrelationships with whole-genome sequence representation by contrastive learning Brief Bioinform.
24(5):bbad239, 2023.

Sato N, Uematsu M, Fujimoto K, Uematsu S, Imoto S.
ggkegg: analysis and visualization of KEGG datautilizing the grammar of graphics. Bioinformatics.
39(10):btad622,2023.
Yokota C, Fujimoto K, Yamakawa N, Kono M, Miyaoka D, Shimohigoshi M, Uematsu M, Watanabe M,Kamei Y, Sugimoto A, Kawasaki N, Yabuno T, Okamura T, Kuroda E, Hamaguchi S, Sato S, Hotomi M,Akeda Y, Ishii KJ, Yasutomi Y, Sunami K, Uematsu
S. Prime-boost-type PspA3 + 2 mucosal vaccine
protects cynomolgus macaques from intratracheal
challenge with pneumococci. Inflamm Regen.
43(1):55,2023.