Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases
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We reconstructed 19,084 prokaryotic and 31,395 viral genomes from 787 Japanese gut metagenomes as Japanese metagenome-assembled genomes (JMAG) and Japanese Virus Database (JVD), which are large microbial genome datasets for a single population. Population-specific enrichment of the Bacillus subtilis and β-porphyranase among the JMAG could derive from the Japanese traditional food natto (fermented soybeans) and nori (laver), respectively. Dairy-related Enterococcus_B lactis and Streptococcus thermophilus were nominally associated with the East Asian-specific missense variant rs671:G>A in ALDH2, which was associated with dairy consumption. Of the species-level viral genome clusters in the JVD, 62.9% were novel. The β crAss-like phage composition was low among the Japanese but relatively high among African and Oceanian peoples. Evaluations of the association between crAss-like phages and diseases showed significant disease-specific associations. Our large catalog of virus-host pairs identified the positive correlation between the abundance of the viruses and their hosts.
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Early evidence indicates dietary microbes can become human microbiome members.
“and early evidence of dietary microbes becoming human microbiome members motivates a more comprehensive investigation of this phenomenon across food types and human populations. 44-47”
From Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome. (2024) · cites this paper as [47]
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Zuo, T., Sun, Y., Wan, Y., Yeoh, Y. K., Zhang, F., Cheung, C. P., Chen, N., Luo, J., Wang, W., Sung, J. J. �., et al. (2020) · Cell Host & Microbe · doi:10.1016/j.chom.2020.08.005 · Cited by 152 · see citing works
Oki, K., Toyama, M., Banno, T., Chonan, O., Benno, Y., & Watanabe, K. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0898-x · Cited by 131 · see citing works
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Tomofuji, Y., Maeda, Y., Oguro-Igashira, E., Kishikawa, T., Yamamoto, K., Sonehara, K., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., et al. (2021) · Annals of the Rheumatic Diseases · doi:10.1136/annrheumdis-2021-220687 · Cited by 75 · see citing works
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Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.
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- Authors
- Tomofuji, Y., Kishikawa, T., Maeda, Y., Ogawa, K., Otake-Kasamoto, Y., Kawabata, S., Nii, T., Okuno, T., Oguro-Igashira, E., Kinoshita, M., Takagaki, M., Oyama, N., Todo, K., Yamamoto, K., Sonehara, K., Yagita, M., Hosokawa, A., Motooka, D., Matsumoto, Y., Matsuoka, H., Yoshimura, M., Ohshima, S., Shinzaki, S., Nakamura, S., Iijima, H., Inohara, H., Kishima, H., Takehara, T., Mochizuki, H., Takeda, K., Kumanogoh, A., & Okada, Y.
- Affiliations
- Institute for Open and Transdisciplinary Research Initiatives (JP)
- Aichi Cancer Center (JP)
- The University of Osaka (JP)
- Kawasaki Medical School (JP)
- Immunology Frontier Research Center, The University of Osaka (JP)
- Suita Municipal Hospital (JP)
- Research Institute for Microbial Diseases, The University of Osaka (JP)
- Osaka Minami Medical Center (JP)
- RIKEN Center for Integrative Medical Sciences (JP)
- Corresponding author
- Tomofuji, Yoshihiko
- ORCID
- Tomofuji, Yoshihiko
- Kishikawa, Toshihiro
- Maeda, Yuichi
- Ogawa, Kotaro
- Kawabata, Shuhei
- Nii, Takuro
- Okuno, Tatsusada
- Oguro-Igashira, Eri
- Kinoshita, Makoto
- Takagaki, Masatoshi
- Oyama, Naoki
- Todo, Kenichi
- Yamamoto, Kenichi
- Sonehara, Kyuto
- Motooka, Daisuke
- Matsumoto, Yuki
- Ohshima, Shiro
- Shinzaki, Shinichiro
- Nakamura, Shota
- Iijima, Hideki
- Inohara, Hidenori
- Kishima, Haruhiko
- Takehara, Tetsuo
- Mochizuki, Hideki
- Takeda, Kiyoshi
- Kumanogoh, Atsushi
- Okada, Yukinori
- Venue
- Cell Genomics
- Publisher
- Elsevier BV
- Published
- 2022-12
- Volume
- 2
- Issue
- 12
- Pages
- 100219
- ISSN
- 2666-979X (ISSN-L)
- PMC
- PMC9903723
- OpenAlex
- W4310552761
- Cited by
- 35
- References
- 106
- Citations by year
- 2026: 7 · 2025: 8 · 2024: 13 · 2023: 7
- FWCI
- 3.86
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Cell Genomics (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Funders
- Takeda Science Foundation
- Japan Agency for Medical Research and Development (JP21ek0109413, JP21ek0410075, JP21gm4010006, JP21km0405211, JP21km0405217)
- Japan Society for the Promotion of Science (19H01021, 20K21834)
- JST (JPMJMS2021, JPMJMS2024)
- Osaka University
- Topics
- Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- virome, natto, nori, Bacillus subtilis, dairy consumption, Enterococcus lactis, Streptococcus thermophilus, crAss-like phages, novel virus, virus-host associations
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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