Publications

▍FY 2024

* First author, ^† Corresponding author

Takewaki D*, Kiguchi Y*, Masuoka H, Manu MS, Raveney BJ, Narushima S, Kurokawa R, Ogata Y, Kimura Y, Sato N, Ozawa Y, Yagishita S, Araki T, Miyake S, Sato W, Suda W^†, Yamamura T^†.
Tyzzerella nexilis strains enriched in mobile genetic elements are involved in progressive multiple sclerosis.
Cell Rep. 2024 Sep 25:114785. https://doi.org/10.1016/j.celrep.2024.114785.
Furuichi M, Kawaguchi T, Pust MM, Yasuma-Mitobe K, Plichta DR, Hasegawa N, Ohya T, Bhattarai SK, Sasajima S, Aoto Y, Tuganbaev T, Yaginuma M, Ueda M, Okahashi N, Amafuji K, Kiridoshi Y, Sugita K, Stražar M, Avila-Pacheco J, Pierce K, Clish CB, Skelly AN, Hattori M, Nakamoto N, Caballero S, Norman JM, Olle B, Tanoue T, Suda W, Arita M, Bucci V, Atarashi K, Xavier RJ, Honda K.
Commensal consortia decolonize Enterobacteriaceae via ecological control.
Nature. 2024 Sep;633(8031):878-886. https://doi.org/10.1038/s41586-024-07960-6.
Liow YJ, Kamimura I, Umezaki M, Suda W, Takayasu L^†.
Dietary fiber induces a fat preference associated with the gut microbiota.
PLoS One. 2024 Jul 10;19(7):e0305849. https://doi.org/10.1371/journal.pone.0305849.
Komaki S, Sahoyama Y, Hachiya T, Koseki K, Ogata Y, Hamazato F, Shiozawa M, Nakagawa T, Suda W, Hattori M, Kawakami E.
Dimension reduction of microbiome data linked Bifidobacterium and Prevotella to allergic rhinitis.
Sci Rep. 2024 Apr 5;14(1):7983.
https://doi.org/10.1038/s41598-024-57934-x.
Masuda S, Gan P, Kiguchi Y, Anda M, Sasaki K, Shibata A, Iwasaki W, Suda W, Shirasu K.Lee, A., & Brown, T.
Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.
Commun Biol. 2024 Mar 27;7(1):357.
https://doi.org/10.1038/s42003-024-05998-w.
Sekiya S, Masuoka H, Mizuno Y, Kibe M, Kosaka S, Natsuhara K, Hirayama K, Inthavong N, Kounnavong S, Tomita S, Takayasu L, Suda W, Yagyu F, Umezaki M.
Asymptomatic Enteric Virus Infections and Association with the Gut Microbiome in Rural Residents of Northern Laos.
Am J Trop Med Hyg. 2024 Mar 12;110(4):759-767.
https://doi.org/10.4269/ajtmh.23-0209.
Watai K*, Suda W*, Kurokawa R, Sekiya K, Hayashi H, Iwata M, Nagayama K, Nakamura Y, Hamada Y, Kamide Y, Fukutomi Y, Nakabayashi T, Tanaka K, Kamita M, Taniguchi M, Hattori M.
Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance.
BMC Microbiol. 2024 Mar 11;24(1):84.
https://doi.org/10.1186/s12866-024-03239-y.
Tamura Y, Takai Y, Miyamoto H, SeokHyun L, Liu Y, Qiu X, Kang LJ, Simasaki Y, Shindo C, Suda W, Ohno H, Oshima Y.
Alteration of shoaling behavior and dysbiosis in the gut of medaka (Oryzias latipes) exposed to 2-μm polystyrene microplastics.
Chemosphere. 2024 Apr;353:141643.
https://doi.org/10.1016/j.chemosphere.2024.141643.
Shibata R, Itoh N, Nakanishi Y, Kato T, Suda W, Nagao M; J-OIT group; Iwata T, Yoshida H, Hattori M, Fujisawa T, Shimojo N, Ohno H.
Gut microbiota and fecal metabolites in sustained unresponsiveness by oral immunotherapy in school-age children with cow's milk allergy.
Allergol Int. 2024 Jan;73(1):126-136.
https://doi.org/10.1016/j.alit.2023.10.001.
Okuhama S, Takahashi H, Nakayama Y, Ogata Y, Suda W^†.
Complete genome sequences of Bifidobacterium faecale strain JCM19861T, isolated from human feces.
Microbiol Resour Announc. 2024 Jan 17;13(1):e0078423.
https://doi.org/10.1128/mra.00784-23.

▍FY 2023

Kurokawa R*, Masuoka H, Takayasu L, Kiguchi Y, Ogata Y, Miura-Kawatsu R, Hattori M, Suda W^†.
Recovery of microbial DNA by agar-containing solution from extremely low-biomass specimens including skin.
Sci Rep. 2023 Nov 11;13(1):19666.
https://doi.org/10.1038/s41598-023-46890-7.
Soeda K, Sasako T, Enooku K, Kubota N, Kobayashi N, Ikushima YM, Awazawa M, Bouchi R, Toda G, Yamada T, Nakatsuka T, Tateishi R, Kakiuchi M, Yamamoto S, Tatsuno K, Atarashi K, Suda W, Honda K, Aburatani H, Yamauchi T, Fujishiro M, Noda T, Koike K, Kadowaki T, Ueki K.
Gut insulin action protects from hepatocarcinogenesis in diabetic mice comorbid with nonalcoholic steatohepatitis.
Nat Commun. 2023 Oct 18;14(1):6584.
https://doi.org/10.1038/s41467-023-42334-y.
Shimomura Y, Sugi Y, Kume A, Tanaka W, Yoshihara T, Matsuura T, Komiya Y, Ogata Y, Suda W, Hattori M, Higurashi T, Nakajima A, Matsumoto M.
Strain-level detection of Fusobacterium nucleatum in colorectal cancer specimens by targeting the CRISPR-Cas region.
Microbiol Spectr. 2023 Dec 12;11(6):e0512322.
https://doi.org/10.1128/spectrum.05123-22.
Nakayasu M, Takamatsu K, Kanai K, Masuda S, Yamazaki S, Aoki Y, Shibata A, Suda W, Shirasu K, Yazaki K, Sugiyama A.
Tomato root-associated Sphingobium harbors genes for catabolizing toxic steroidal glycoalkaloids.
mBio. 2023 Oct 31;14(5):e0059923.
https://doi.org/10.1128/mbio.00599-23.
Takeuchi T, Kubota T, Nakanishi Y, Tsugawa H, Suda W, Kwon AT, Yazaki J, Ikeda K, Nemoto S, Mochizuki Y, Kitami T, Yugi K, Mizuno Y, Yamamichi N, Yamazaki T, Takamoto I, Kubota N, Kadowaki T, Arner E, Carninci P, Ohara O, Arita M, Hattori M, Koyasu S, Ohno H.
Gut microbial carbohydrate metabolism contributes to insulin resistance.
Nature. 2023 Sep;621(7978):389-395.
https://doi.org/10.1038/s41586-023-06466-x.
Kawamoto S, Uemura K, Hori N, Takayasu L, Konishi Y, Katoh K, Matsumoto T, Suzuki M, Sakai Y, Matsudaira T, Adachi T, Ohtani N, Standley DM, Suda W, Fukuda S, Hara E.
Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota.
Nat Cell Biol. 2023 Jun;25(6):865-876.
https://doi.org/10.1038/s41556-023-01145-5.
Ito T, Nakanishi Y, Shibata R, Sato N, Jinnohara T, Suzuki S, Suda W, Hattori M, Kimura I, Nakano T, Yamaide F, Shimojo N, Ohno H.
The propionate-GPR41 axis in infancy protects from subsequent bronchial asthma onset.
Gut Microbes. 2023 Jan-Dec;15(1):2206507.
https://doi.org/10.1080/19490976.2023.2206507.
Aiyoshi T*, Kakihara T*, Watanabe E, Tanaka N, Ogata Y, Masuoka H, Kurokawa R, Fujishiro J, Masumoto K, Suda W^†.
A comprehensive microbial analysis of pediatric patients with acute appendicitis.
J Microbiol Immunol Infect. 2023 Aug;56(4):695-704.
https://doi.org/10.1016/j.jmii.2023.03.006.
Miyamoto H, Shigeta K, Suda W, Ichihashi Y, Nihei N, Matsuura M, Tsuboi A, Tominaga N, Aono M, Sato M, Taguchi S, Nakaguma T, Tsuji N, Ishii C, Matsushita T, Shindo C, Ito T, Kato T, Kurotani A, Shima H, Moriya S, Wada S, Horiuchi S, Satoh T, Mori K, Nishiuchi T, Miyamoto H, Kodama H, Hattori M, Ohno H, Kikuchi J, Hirai MY.
An agroecological structure model of compost-soil-plant interactions for sustainable organic farming.
ISME Commun. 2023 Mar 31;3(1):28.
https://doi.org/10.1038/s43705-023-00233-9.
Ogata Y, Watanabe K, Takemine S, Kaida K, Tanokura M, Suda W^†.
Complete Genome Sequences of Polynucleobacter sp. Subcluster PnecA Strains SHI2 and SHI8, Isolated from an Oligotrophic-Dystrophic Lake in Japan.
Microbiol Resour Announc. 2023 Apr 18;12(4):e0003023.
https://doi.org/10.1128/mra.00030-23.
Ogata Y, Watanabe K, Takemine S, Shindo C, Kurokawa R, Suda W^†.
Complete Genome Sequences of Three Limnohabitans sp. (Lhab-A3) Strains, INBF002, TEGF004, and MORI2, Isolated from Two Lakes and a River in Japan.
Microbiol Resour Announc. 2023 Mar 16;12(3):e0129622.
https://doi.org/10.1128/mra.01296-22.
Ogata Y, Watanabe K, Takemine S, Kaida K, Tanokura M, Suda W^†.
Complete Genome Sequence of Aurantimicrobium sp. Strain INA4, Isolated from an Oligotrophic Lake in Japan.
Microbiol Resour Announc. 2023 Mar 16;12(3):e0124722.
https://doi.org/10.1128/mra.01247-22.
Ogata Y, Watanabe K, Takemine S, Shindo C, Kurokawa R, Suda W^†.
Complete Genome Sequences of Three Polynucleobacter sp. Subcluster PnecC Strains, KF022, KF023, and KF032, Isolated from a Shallow Eutrophic Lake and a River in Japan.
Microbiol Resour Announc. 2023 Mar 16;12(3):e0123422.
https://doi.org/10.1128/mra.01234-22.