RIKEN-JSS Joint Symposium- Toward applied symbiosis biology 16:00-16:10: Ken Shirasu(RIKEN CSRS, Plant Immunity Research Group)
Opening remarks - Introduction of iSym
16:10-16:40: Hiroshi OHNO(RIKEN IMS, Laboratory for Intestinal Ecosystem)“Host-gut microbiota interaction: from humans to livestock”
16:40-17:10: Youxian Li/Kenya HONDA(RIKEN IMS, Laboratory for Gut Homeostasis)“Trypsin-degrading Paraprevotella maintains intestinal homeostasis”
17:10-17:40: Yasunori ICHIHASHI(RIKEN BRC, Plant-Microbe Symbiosis Research and Development Team)“Field multi-omics dissects an agroecosystem”
17:40-18:10: Moriya OHKUMA(RIKEN BRC, Microbe Division)“Cultured microbial resources and single-cell genomics of yet-uncultured forintegrated symbiology”
18:10-18:20: Ken-ichiro Ishida(Tsukuba University)
Closing remarks - Invitation for Japan Symbiosis Society

18:30-: Get-together party with beverages at Cafeteria

Abstracts
Host-gut microbiota interaction: from humans to livestock
Hiroshi Ohno1,2, Hirokuni Miyamoto2,3,4
1

Laboratory for Intestinal Ecosystem, RIKEN Center for Integrative Medical Sciences

2Intestinal Microbiota Project, Kanagawa Institute of Industrial Science and Technology

3Biochemistry Laboratory, Graduate School of Advanced Integration Science, Chiba University

4Japan Eco-science (Nikkan Kagaku) Co. Ltd

The gastrointestinal mucosa is always exposed to enormous numbers of commensal bacteria,
gut microbiota. This gut microbiota is the most in the colon, with more than 40 trillions in
number in humans. With some 700,000 genes, the gut microbiota has a very complex metabolic
system as a whole, and interacts with the host to constitute the unique gut ecosystem. With this,they deeply impact the host physiological and pathological conditions. In fact, accumulating
evidence has indicated that gut microbiota affects the pathogenesis of various diseases, ranging
from gastrointestinal, immunological, metabolic, to even neurological disorders.
To understand complex host-gut microbiota interaction, we employ “integrated omics approach”.
We are applying this approach to search for the gut microbiota-related pathogenic biomarkers
for pediatric allergies and type 2 diabetes mellitus (T2D). For allergies, birth cohort is examinedin search of biomarkers for atopic dermatitis, food allergies, and bronchial asthma, incollaboration with Dr. Naoki Shimojo (Chiba University, Chiba, Japan). T2D study is an IMS
center project involving multiple IMS laboratories, in collaboration with the University ofTokyo Hospital for the recruitment of participants from those who took a complete medicalcheckup.
We are also studying the gut microbiota of livestock. WHO warns that antimicrobial resistance(AMR) can be a biggest threat for humans; they predict that infection with misuse and overuseof antimicrobials is accelerating AMR. Majority of antimicrobials are used for animals
worldwide, including Japan. In order to reduce the use of antibiotics in livestock, we are trying
to control their gut microbiota with probiotics.

Trypsin-degrading Paraprevotella maintains intestinal homeostasis
Youxian Li1,§, Eiichiro Watanabe1,2,3,§, Yusuke Kawashima4, §, Zhujun Wang1,2, Seiko
Narushima1, Keita Nishiyama2, Sean Kearney2, Wataru Suda1, Sasajima Satoshi2, Kazuto
Watanabe6, Brian A. Klein7, Atsushi Shiota2,6, Jason M. Norman7, Bernat Olle7, Bruce Roberts7,Koji Atarashi1,2,6, Masahira Hattori1,5, Osamu Ohara4, Kenya Honda1,2,6*
1

RIKEN Center for Integrative Medical Sciences

2Department of Microbiology and Immunology, Keio University School of Medicine

3Pediatric Surgery, The University Tokyo

4

Department of Genome Research and Development, Kazusa DNA Research Institute5

Cooperative Major in Advanced Health Science, Graduate School of Advanced Science andEngineering, Waseda University
6

JSR-Keio University Medical and Chemical Innovation Center, Keio University School ofMedicine
7

Vedanta Biosciences, Cambridge§These authors equally contributed to this work

The gastrointestinal tract is constitutively exposed to proteases, including a serineprotease trypsin originated from the pancreas. Elevated trypsin levels in the lower intestine havebeen implicated in pathological conditions including inflammatory bowel disease (IBD). Here
we show that trypsin is degraded in the lower intestine by members of the gut microbiota,Paraprevotella. After passing through the small intestine, trypsin activity is markedly reduced in
the cecum and colon of SPF mice, and germ-free (GF) mice have considerably higher fecal

trypsin levels than SPF mice. We have successfully isolated Paraprevotella clara andParaprevotella xylaniphila from the microbiome of healthy human donors as potent
trypsin-degrading species. Mechanistically, trypsin specifically binds to the surface ofParaprevotella, and binding of trypsin to Paraprevotella promotes its autolysis. Intestinal
colonization with Paraprevotella and consequent reduction of trypsin contribute to themaintenance of mucosal integrity and protect colon tissue from invasion by a colitogenic
pathogen, Citrobacter rodentium. Such a microbiome-based approach targeting excessive
proteases may represent a therapeutic strategy for colonic diseases through restoring intestinal
homeostasis.

Field multi-omics dissects an agroecosystem
Yasunori Ichihashi
RIKEN BRC, Plant-Microbe Symbiosis Research and Development Team

Both inorganic fertilizer inputs and crop yields have increased globally, with the concurrent
increase in the pollution of water bodies due to nitrogen leaching from soils. Designingagroecosystems that are environmentally friendly is urgently required. Since agroecosystems arehighly complex and consist of entangled webs of interactions between plants, microbes andsoils, identifying critical components in crop production remain elusive. To understand thenetwork structure in agroecosystems engineered by several farming methods including
environmentally-friendly soil solarization, we utilized a multi-omics approach on a field plantedwith Brassica rapa. We found that the soil solarization showed an increase in plant shootbiomass irrespective of the type of fertilizer applied. Our multi-omics and integrated informatics
revealed complex interactions in the agroecosystem showing multiple network modules
represented by plant traits heterogeneously associated with soil metabolites, minerals andmicrobes. Unexpectedly, we identified soil organic nitrogen induced by soil solarization as oneof the key components to increase crop yield. A germ-free plant in vitro assay confirmed thatspecific organic nitrogen, namely alanine and acetylcholine, directly increased plant biomass;alanine was utilized as a nitrogen source, while acetylcholine behaved as a biologically activecompound. Thus, our study provides evidence at the agroecosystem level that organic nitrogenshows a significant contribution to plant growth, leading a potential solution to make cropproduction more sustainable by utilizing the natural nutrient cycle.

Cultured microbial resources and single-cell genomics of yet-uncultured for
integrated symbiology
Moriya Ohkuma
RIKEN BRC, Japan Collection of Microorganisms

A major obstacle of the studies on symbiosis is the formidable difficulty culturing relevant
microbial symbionts. Development of next generation technologies and availability ofrepresentative cultured strains of symbionts are keys for understanding the nature of symbiosis
and its future application.
Flagellated protists (single-cell eukaryotes) and their associated bacteria are predominantcomponents of the complex microbial community in the gut of termites. The associations arecrucial for decomposition of recalcitrant lignocellulose and thriving of the host on its nutrient
poor diet. We have been investigating the associated bacteria with single-cell genomics and thegut protists with single-cell transcriptomics, respectively. These culture-independent approaches,by revealing the functional potentials of each partner, gradually advance our understanding how
the symbiotic relationships work efficiently.
In addition, as a world-leading microbial resource center, we have been collecting cultured,taxonomically identified representatives of symbionts from a variety of isolation sources.
Enrichment of such a collection of microbial symbionts, characterizations of them, and opening
to public are surely beneficial to enhance research in symbiology.