Original Articles


Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. (2024) Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 9(2): e01123-23.

García-Lozano M, Henzler C, Porras MÁG, Pons I, Berasategui A, Lanz C, Budde H, Oguchi K, Matsuura Y, Pauchet Y, Goffredi S, Fukatsu T, Windsor D, Salem H. (2024) Paleocene origin of a streamlined digestive symbiosis in leaf beetles. Current Biology 34: 1–14.

Koga R, Moriyama M, Nozaki T, Fukatsu T. (2024) Genome analysis of “Candidatus Aschnera chinzeii”, the bacterial endosymbiont of the blood-sucking bat fly Penicillidia jenynsii (Insecta: Diptera: Nycteribiidae). Frontiers in Microbiology 14: 1336919.


Wang Y, Morishima T, Sezaki M, Sato R, Nakato G, Fukuda S, Kobiyama K, Ishii KJ, Li Y, Takizawa H. (2023) Akkermansia muciniphila induces slow extramedullary hematopoiesis via cooperative IL-1R/TLR signals. EMBO Reports: e57485.

Kanai Y, Tsuru S, Furusawa C. (2023) Insertion sequences: Simple mobile elements with rich ecological and evolutionary structures. Currrent Opinion in Systems Biology 36: 100481.

Genthon A, Nozoe T, Peliti L, Lacoste D. (2023) Cell lineage statistics with incomplete population trees. PRX Life 1: 013014.

Nishida K, Adachi H, Moriyama M, Futahashi R, Hanson PE, Kondo S. (2023) Butterfly wing color made of pigmented liquid Author links open overlay panel. Cell Reports 42(8): 112917.

Arai H, Anbutsu H, Nishikawa Y, Kogawa M, Ishii K, Hosokawa M, Lin S, Ueda M, Nakai M, Kunimi Y, Harumoto T, Kageyama D, Takeyama H, Inoue M. (2023) Combined actions of bacteriophage-encoded genes in Wolbachia-induced male lethality. iScience 26(6): 106842.

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. (2023) Bacterial induction of B cell senescence promotes age-related changes in the gut microbiota. Nature Cell Biology 25(6): 865-876.

Koganezawa Y, Wakamoto Y, Sato M, Umetani M. (2023) Detecting photoactivatable Cre-mediated gene deletion efficiency in Escherichia coli. Bio-protocol 13(11): e4685.

Tsutsumi M, Saito N, Koyabu D, Furusawa C. (2023) A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape. NPJ Systems Biology and Applications 9: 30.

Zhu X, Sakamoto S, Ishii C, Smith MD, Ito K, Obayashi M, Unger L, Hasegawa Y, Kurokawa S, Kishimoto T, Li H, Hatano S, Wang TH, Yoshikai Y, Kano SI, Fukuda S, Sanada K, Calabresi PA, Kamiya A. (2023) Dectin-1 signaling on colonic γδ T cells promotes psychosocial stress responses. Nature Immunology 24(4): 625-636.

Omachi Y, Saito N, Furusawa C. (2023) Rare-event sampling analysis uncovers the fitness landscape of the genetic code. PLOS Computational Biology 19(4): e1011034.

Takano S, Takahashi H, Yama Y, Miyazaki R, Furusawa C, Tsuru S. (2023) Inference of transcriptome signatures of Escherichia coli in long-term stationary phase. Scientific Report 13(1): 5647.

Uchida Y, Takeda H, Furusawa C, Irie N. (2023) Stability in gene expression and body-plan development leads to evolutionary conservation. EvoDevo 14(1): 4.

Seike T, Takekata H, Uchida Y, Sakata N, Furusawa C, Matsuda F. (2023) Wickerhamiella bidentis sp. nov., a novel yeast species isolated from flowers and insects in Japan. International Journal of Systenatic and Evolutionary Microbiology 73(3): 005739.

Oishi S, Moriyama M, Mizutani M, Futahashi R, Fukatsu T. (2023) Regulation and remodeling of microbial symbiosis in insect metamorphosis. Proceedings of the National Academy of Sciences of the United States of America 120(40): e2304879120.

Harumoto T. (2023) Self-stabilization mechanism encoded by a bacterial toxin facilitates reproductive parasitism. Current Biology 33(18): 4021-4029.

Oishi S, Moriyama M, Fukatsu T. (2023) Structural remodeling of midgut symbiotic organ and altered food flow upon metamorphosis of the stinkbug Plautia stali. Applied Entomology and Zoology 58: 393–399.

Moriyama M, Nishide Y, Toyoda A, Ito T, Fukatsu T. (2023) Complete genomes of mutualistic bacterial co-symbionts “Candidatus Sulcia muelleri” and “Candidatus Nasuia deltocephalinicola” of the rice green leafhopper Nephotettix cincticeps. Microbiology Resource Announcements 12: e00353-23.

Fukatsu T, Gottlieb Y, Duron O, Graf J. (2023) Microbial associates of blood-sucking arthropods and other animals: relevance to their physiology, ecology and evolution. Frontiers in Microbiology 14: 1256275.

Salem H, Biedermann P, Fukatsu T. (2023) Diversity of beetles and associated microorganisms. Frontiers in Microbiology 14: 1252736.

Tanaka K, Tanigawa N, Song I, Komatsu T, Kuriki Y, Tanaka Y, Fukudo S, Urano Y, Fukuda S. (2023) A protease activity-based machine-learning approach as a complementary tool for conventional diagnosis of diarrhea-predominant irritable bowel syndrome. Frontiers in Microbiology 14: 1179534.

Kiefer JST, Bauer E, Okude G, Fukatsu T, Kaltenpoth M, Engl T. (2023) Cuticle supplementation and nitrogen recycling by a dual bacterial symbiosis in a family of xylophagous beetles. The ISME Journal 17: 1029-1039.

Hirota B, Koga R, Fukatsu T. (2023) Localization of symbiotic bacteria in embryogenesis of the lesser grain borer Rhyzopertha dominica and the African powderpost beetle Lyctus africanus (Coleoptera: Bostrichidae). Applied Entomology and Zoology 58(3): 291–296.

*Nagai M, *Moriyama M, *Ishii C, Mori H, Watanabe H, Nakahara T, Yamada T, Ishikawa D, Ishikawa T, Hirayama A, Kimura I, Nagahara A, Naito T, Fukuda S, Ichinohe T. (2023) High body temperature increases gut microbiota-dependent host resistance to influenza A virus and SARS-CoV-2 infection. Nature Communications 14: 3863.
(*Equal contributions)

Oishi S, Harumoto T, Okamoto-Furuta K, Moriyama M, Fukatsu T. (2023) Mechanisms underpinning morphogenesis of a symbiotic organ specialized for hosting an indispensable microbial symbiont in stinkbugs. mBio 14(2): e00522-23.

*Kageyama D, *Harumoto T, Nagamine K, Fujiwara A, Sugimoto T, Jouraku A, Tamura M, Katoh T, Watada M. (2023) A male-killing gene encoded by a symbiotic virus of Drosophila. Nature Communications 14(1):1357. (*Equal contributions)

Morita H, Kano C, Ishii C, Kagata N, Ishikawa T, Hirayama A, Uchiyama Y, Hara S, Nakamura T, Fukuda S. (2023) Bacteroides uniformis and its preferred substrate, α-cyclodextrin, enhance endurance exercise performance in mice and human males. Science Advances 9: add2120.


Miyaho K, Sanada K, Kurokawa S, Tanaka A, Tachibana T, Ishii C, Noda Y, Nakajima S, Fukuda S, Mimura M, Kishimoto T, Iwanami A. (2022) The potential impact of age on gut microbiota in patients with major depressive disorder: a secondary analysis of the prospective observational study. Journal of Personalized Medicine 12(11): 1827.

Iwasawa J, Maeda T, Shibai A, Kotani H, Kawada M, Furusawa C. (2022) Analysis of the evolution of resistance to multiple antibiotics enables prediction of the Escherichia coli phenotype-based fitness landscape. PLOS Biology 20(12): e3001920.

Yamauchi, S., Nozoe, T., Okura, R., Kussell, E., Wakamoto, Y. (2022) A unified framework for measuring selection on cellular lineages and traits. eLife 11: e72299.

Kiyama H, Kakizawa S, Sasajima Y, Tahara Y, Miyata M. (2022) Reconstitution of a minimal motility system based on Spiroplasma swimming by two bacterial actins in a synthetic minimal bacterium. Science Advances 8: eabo7490.

Sezaki M, Hayashi Y, Nakato G, Wang Y, Nakata S, Biswas S, Morishima T, Fakruddin M, Moon J, Ahn S, Kim P, Miyamoto Y, Baba H, Fukuda S, Takizawa H. (2022) Hematopoietic stem and progenitor cells integrate microbial signals to promote post-inflammation gut tissue repair. The EMBO Journal 41(22): e110712.

Nishide Y, Nagamine K, Kageyama D, Moriyama M, Futahashi R, Fukatsu T. (2022) A new antimicrobial peptide, Pentatomicin, from the stinkbug Plautia stali. Scientific Reports 12: 16503.

*Kakizawa S, *Hosokawa T, Oguchi K, Miyakoshi K, Fukatsu T. (2022) Spiroplasma as facultative bacterial symbionts of stinkbugs. Frontiers in Microbiology 13: 1044771.
(*Equal contributions)

Shibai A, Kotani H, Kawada M, Yokoi N, Furusawa C. (2022) Development of a device that generates a temperature gradient in a microtiter plate for microbial culture. SLAS Technology 27(5): 279-283.

Moriyama M, Fukatsu T. (2022) Host’s demand for essential amino acids is compensated by an extracellular bacterial symbiont in a hemipteran insect model. Frontiers in Physiology 13: 1028409.

Yakabe K, Higashi S, Akiyama M, Mori H, Murakami T, Toyoda A, Sugiyama Y, Kishino S, Okano K, Hirayama A, Gotoh A, Li S, Mori T, Katayama T, Ogawa J, Fukuda S, Hase K, Kim YG. (2022) Dietary-protein sources modulate host susceptibility to Clostridioides difficile infection through the gut microbiota. Cell Reports 40(11): 111332.

Yoshida Y, Shimizu I, Shimada A, Nakahara K, Yanagisawa S, Kubo M, Fukuda S, Ishii C, Yamamoto H, Ishikawa T, Kano K, Aoki J, Katsuumi G, Suda M, Ozaki K, Yoshida Y, Okuda S, Ohta S, Okamoto S, Minokoshi Y, Oda K, Sasaoka T, Abe M, Sakimura K, Kubota Y, Yoshimura N, Kajimura S, Zuriaga M, Walsh K, Soga T, Minamino T. (2022) Brown adipose tissue dysfunction promotes heart failure via a trimethylamine N-oxide-dependent mechanism. Scientific Reports 12: 14883.

Shibai A, Kotani H, Sakata N, Furusawa C, Tsuru S. Purifying selection enduringly acts on the sequence evolution of highly expressed proteins in Escherichia coli. G3: Genes, Genomes, Genetics 12(11): jkac235.

Koga R, Moriyama M, Onodera-Tanifuji N, Ishii Y, Takai H, Mizutani M, Oguchi K, Okura R, Suzuki S, Gotoh Y, Hayashi T, Seki M, Suzuki Y, Nishide Y, Hosokawa T, Wakamoto Y, Furusawa C, Fukatsu T. (2022) Single mutation makes Escherichia coli an insect mutualist. Nature Microbiology 7(8): 1141-1150.

*Nishide Y, *Oguchi K, Murakami M, Moriyama M, Koga R, Fukatsu T (2022) Endosymbiotic bacteria of the boar louse Haematopinus apri (Insecta: Phthiraptera: Anoplura). Frontiers in Microbiology 13: 962252.
(*Equal contributions)

Yukawa-Muto Y, Kamiya T, Fujii H, Mori H, Toyoda A, Sato I, Konishi Y, Hirayama A, Hara E, Fukuda S, Kawada N, Ohtani N. (2022) Distinct responsiveness to rifaximin in patients with hepatic encephalopathy depends on functional gut microbial species. Hepatology Communications 6(8): 2090-2104.

Tanaka Y, Yamashita R, Kawashima J, Mori H, Kurokawa K, Fukuda S, Gotoh Y, Nakamura K, Hayashi T, Kasahara Y, Sato Y, Fukudo S. (2022) Omics profiles of fecal and oral microbiota change in irritable bowel syndrome patients with diarrhea and symptom exacerbation. Journal of Gastroenterology 57: 748-760.

Jangid A, Fukuda S, Seki M, Suzuki Y, Taylor TD, Ohno H, Prakash T. (2022) Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene. Scientific Reports 12: 10812.

Yamagishi R, Kamachi F, Nakamura M, Yamazaki S, Kamiya T, Takasugi M, Cheng Y, Nonaka Y, Yukawa-Muto Y, Thuy LTT, Harada Y, Arai T, Loo TM, Yoshimoto S, Ando T, Nakajima M, Taguchi H, Ishikawa T, Akiba H, Miyake S, Kubo M, Iwakura Y, Fukuda S, Chen WY, Kawada N, Rudensky A, Nakae S, Hara E, Ohtani N. (2022) Gasdermin D-mediated release of IL-33 from senescent hepatic stellate cells promotes obesity-associated hepatocellular carcinoma. Science Immunology 7(72): eabl7209.

*Moriyama M., *Hayashi T., Fukatsu T. (2022) A mucin protein predominantly expressed in the female-specific symbiotic organ of the stinkbug Plautia stali. Scientific Reports 12: 7782.
(*Equal contributions)

Harumoto T., Fukatsu T. (2022) Perplexing dynamics of Wolbachia proteins for cytoplasmic incompatibility. PLOS Biology 20(5): e3001644.

Koganezawa Y, Umetani M, Sato M, Wakamoto Y (2022) History-dependent physiological adaptation to lethal genetic modification under antibiotic exposur. eLife 11: e74486.

Jangid A, Fukuda S, Suzuki Y, Taylor TD, Ohno H, Prakash T. (2022) Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice. Scientific Reports 12: 6748.

Kure A, Tsukimi T, Ishii C, Aw W, Obana N, Nakato G, Hirayama A, Kawano H, China T, Shimizu F, Nagata M, Isotani S, Muto S, Horie S, Fukuda S. (2022) Gut environment changes due to androgen deprivation therapy in patients with prostate cancer. Prostate Cancer and Prostatic Diseases: DOI: 10.1038/s41391-022-00536-3.

Shiroma H, Shiba S, Erawijantari PP, Takamaru H, Yamada M, Sakamoto T, Kanemitsu Y, Mizutani S, Soga T, Saito Y, Shibata T, Fukuda S, Yachida S, Yamada T (2022) Surgical treatment for colorectal cancer partially restores gut microbiome and metabolome traits. mSystems: e00018-22.

Ishihara S, Sato T, Fujikado N, Miyazaki H, Yoshimoto T, Yamamoto H, Fukuda S, Katagiri K (2022) Rap1 prevents colitogenic Th17 cell expansion and facilitates Treg cell differentiation and distal TCR signaling. Communications Biology 5: 206.

Jangid A, Fukuda S, Kato T, Seki M, Suzuki Y, Taylor TD, Ohno H, Prakash T (2022) Impact of dietary fructooligosaccharides (FOS) on murine gut microbiota and intestinal IgA secretion. 3 Biotech 12: 56.

Kanai Y, Tsuru S, Furusawa C (2022) Experimental demonstration of operon formation catalyzed by insertion sequence. Nucleic Acids Research gkc004: 6511971.

Fukumori K, Oguchi K, Ikeda H, Shinohara T, Tanahashi M, Moriyama M, Koga R, Fukatsu T (2022) Evolutionary dynamics of host organs for microbial symbiosis in tortoise leaf beetles (Coleoptera: Chrysomelidae: Cassidinae). mBio 13(1): e03691-21.

Maruyama Y, Nishimoto Y, Umezawa K, Kawamata R, Ichiba Y, Tsutsumi K, Kimura M, Murakami S, Kakizawa Y, Kumagai T, Yamada T, Fukuda S (2022) Comparison of oral metabolome profiles of stimulated saliva, unstimulated saliva, and mouth-rinsed water. Scientific Reports 12: 689.


Furusawa C, Tanabe K, Ishii C, Kagata N, Tomita M, Fukuda S (2021) Decoding gut microbiota by imaging analysis of fecal samples. iScience 24: 103481.

Seike T, Sakata N, Shimoda C, Niki H, Furusawa C (2021) The sixth transmembrane region of a pheromone G-protein coupled receptor, Map3, is implicated in discrimination of closely related pheromones in Schizosaccharomyces pombe. Genetics 219(4): iyab150.

Connell S, Kawashima M, Nakamura S, Imada T, Yamamoto H, Tsubota K, Fukuda S (2021) Lactoferrin ameliorates dry eye disease potentially through enhancement of short-chain fatty acid production by gut microbiota in mice. International Journal of Molecular Sciences 22(22): 12384.

Yokoyama Y, Shinohara K, Kitamura N, Nakamura A, Onoue A, Tanaka K, Hirayama A, Aw W, Nakamura S, Ogawa Y, Fukuda S, Tsubota K, Watanabe M (2021) Metabolic effects of bee larva-derived protein in mice: assessment of an alternative protein source. Foods 10(11): 2642.

Shimaya T, Okura R, Wakamoto Y, Takeuchi K A (2021) Scale invariance of cell size fluctuations in starving bacteria. Communications Physics 4: 238.

Nishiumi F, Kawai Y, Nakura Y, Yoshimura M, Wu HN, Hamaguchi M, Kakizawa S, Suzuki Y, Glass JI, Yanagihara I (2021) Blockade of endoplasmic reticulum stress-induced cell death by Ureaplasma parvum vacuolating factor. Cellular Microbiology 23(12): e13392.

Kurokawa S, Tomizawa Y, Miyaho K, Ishii D, Takamiya A, Ishii C, Sanada K, Fukuda S, Mimura M, Kishimoto T (2021) Fecal microbial and metabolomic change during treatment course for depression: an observational study. Journal of Psychiatric Research 140: 45-52.

Ejima R, Akiyama M, Sato H, Tomioka S, Yakabe K, Kimizuka T, Seki N, Fujimura Y, Hirayama A, Fukuda S, Hase K, Kim YG (2021) Seaweed dietary fiber sodium alginate suppresses the migration of colonic inflammatory monocytes and diet-induced metabolic syndrome via the gut microbiota. Nutrients 13(8): 2812.

Maeda T, Shibai A, Yokoi N, Tarusawa Y, Kawada M, Kotani H, Furusawa C (2021) Mutational property of newly identified mutagen L-glutamic acid γ-hydrazide in Escherichia coli. Mutation Research 823: 111759.

Maeda T, Kawada M, Sakata N, Kotani H, Furusawa C (2021) Laboratory evolution of Mycobacterium on agar plates for analysis of resistance acquisition and drug sensitivity profiles. Scientific Reports 11: 15136.

Maeda T, Kotani H, Furusawa C (2021) Morphological change of coiled bacterium Spirosoma linguale with acquisition of β-lactam resistance. Scientific Reports 11: 13278.

*Koga R, *Tanahashi M, Nikoh N, Hosokawa T, Meng XY, Moriyama M, Fukatsu T (2021) Host’s guardian protein counters degenerative symbiont evolution. Proceedings of the National Academy of Sciences of the United States of America 118 (25): e2103957118. (* Equal contributions)

Kiefer JST, Batsukh S, Bauer E, Hirota B, Weiss B, Wierz JC, Fukatsu T, Kaltenpoth M, Engl T (2021) Inhibition of a nutritional endosymbiont by glyphosate abolishes mutualistic benefit on cuticle synthesis in Oryzaephilus surinamensis. Communications Biology 4: 554.

Sato S, Shimizu E, He J, Ogawa M, Asai K, Yazu H, Rusch R, Yamane M, Yang F, Fukuda S, Kawakami Y, Tsubota K, Ogawa Y (2021) Positive effects of oral antibiotic administration in murine chronic graft-versus-host disease. International Journal of Molecular Sciences 22(7): 3745.

Nakamura A, Kurihara S, Takahashi D, Ohashi W, Nakamura Y, Kimura S, Onuki M, Kume A, Sasazawa Y, Furusawa Y, Obata Y, Fukuda S, Saiki S, Matsumoto M, Hase K (2021) Symbiotic polyamine metabolism regulates epithelial proliferation and macrophage differentiation in the colon. Nature Communications 12: 2105.

*Nishino T, *Hosokawa T, Meng XY, Koga R, Moriyama M, Fukatsu T (2021) Environmental acquisition of gut symbiotic bacteria in the saw-toothed stinkbug Megymenum gracilicorne (Hemiptera: Pentatomoidea: Dinidoridae). Zoological Science 38 (3): 213-222. (*Equal contributions)

Fukatsu T (2021) The long and winding road for symbiont and yolk protein to host oocyte. mBio 12(1): e02997-20.

Seita A, Nakaoka H, Okura R, Wakamoto Y (2021) Intrinsic growth heterogeneity of mouse leukemia cells underlies differential susceptibility to a growth-inhibiting anticancer drug. PLoS One 16(2): e0236534.

Tomizawa Y, Kurokawa S, Ishii D, Miyaho K, Ishii C, Sanada K, Fukuda S, Mimura M, Kishimoto T (2021) Effects of psychotropics on the microbiome in patients with depression and anxiety: Considerations in a naturalistic clinical setting. International Journal of Neuropsychopharmacology 24(2): 97-107.

Nishide Y, Kageyama D, Tanaka Y, Yokoi K, Jouraku A, Futahashi R, Fukatsu T (2021)
Effectiveness of orally-delivered double-stranded RNA on gene silencing in the stinkbug Plautia stali. PLoS One 16(1): e0245081.


Maeda T, Iwasawa J, Kotani H, Sakata N, Kawada M, Horinouchi T, Sakai A, Tanabe K, Furusawa C (2020) High-throughput laboratory evolution reveals evolutionary constraints in Escherichia coli. Nature Communications 11: 5970.

Ogawa Y, Miyoshi C, Obana N, Yajima K, Hotta-Hirashima N, Ikkyu A, Kanno S, Soga T, Fukuda S, Yanagisawa M (2020) Gut microbiota depletion by chronic antibiotic treatment alters the sleep/wake architecture and sleep EEG power spectra in mice. Scientific Reports 10: 19554.

Hirota B, Meng XY, Fukatsu T (2020) Bacteriome-associated endosymbiotic bacteria of Nosodendron tree sap beetles (Coleoptera: Nosodendridae). Frontiers in Microbiology 11: 588841.

Nikoh N., Tsuchida T., Koga R., Oshima K., Hattori M., Fukatsu T (2020) Genome analysis of "Candidatus Regiella insecticola" strain TUt, facultative bacterial symbiont of the pea aphid Acyrthosiphon pisum. Microbiology Resource Announcements 9: e00598-20.

Caballero-Flores G, Pickard JM, Fukuda S, Inohara N, Núñez G (2020) An enteric pathogen subverts colonization resistance by evading competition for amino acids in the gut. Cell Host & Microbe 28(4): 526-533.

Nakamura A, Yokoyama Y, Tanaka K, Benegiamo G, Hirayama A, Zhu Q, Kitamura N, Sugizaki T, Morimoto K, Itoh H, Fukuda S, Auwerx J, Tsubota K, Watanabe M (2020) Asperuloside improves obesity and type 2 diabetes through modulation of gut microbiota and metabolic signaling. iScience 23(9): 101522.

Salem H, Kirsch R, Pauchet Y, Berasategui A, Fukumori K, Moriyama M, Cripps M, Windsor D, Fukatsu T, Gerardo NM (2020) Symbiont digestive range reflects host plant breadth in herbivorous beetles. Current Biology 30(15): 2875-2886.

Mishima E, Ichijo M, Kawabe T, Kikuchi K, Akiyama Y, Toyohara T, Suzuki T, Suzuki C, Asao A, Ishii N, Fukuda S, Abe T (2020) Germ-free conditions modulate host purine metabolism, exacerbating adenine-induced kidney damage. Toxins 12(9): E547.

Yang J, Yang Y, Ishii M, Nagata M, Aw W, Obana N, Tomita M, Nomura N, Fukuda S (2020) Does the gut microbiota modulate host physiology through polymicrobial biofilms? Microbes and Environment 35(3): ME20037.

Horinouchi T, Maeda T, Kotani H, Furusawa C (2020) Suppression of antibiotic resistance evolution by single-gene deletion. Scientific Reports 10: 4178.

Toju H, Abe MS, Ishii C, Hori Y, Fujita H, Fukuda S (2020) Scoring species for synthetic community design: network analyses of functional core microbiomes. Frontiers in Microbiology 11: 1361.

Tsukimi T, Watabe T, Tanaka K, Sato MP, Suzuki H, Tomita M, Fukuda S (2020) Draft genome sequences of Bifidobacterium animalis consecutively isolated from healthy Japanese individuals. Journal of Genomics 8: 37-42.

Erawijantari PP, Mizutani S, Shiroma H, Shiba S, Nakajima T, Sakamoto T, Saito Y, Fukuda S, Yachida S, Yamada T (2020) Influence of gastrectomy for gastric cancer treatment on faecal microbiome and metabolome profiles. Gut 69(8): 1404-1415.

Jangid A, Fukuda S, Seki M, Horiuchi T, Suzuki Y, Taylor TD, Ohno H, Prakash T (2020) Association of colitis with gut-microbiota dysbiosis in clathrin adapter AP-1B knockout mice. PLoS One 15(3): e0228358.

Nagao-Kitamoto H, Leslie JL, Kitamoto S, Jin C, Thomsson KA, Gillilland MG 3rd, Kuffa P, Goto Y, Jenq RR, Ishii C, Hirayama A, Seekatz AM, Martens EC, Eaton KA, Kao JY, Fukuda S, Higgins PDR, Karlsson NG, Young VB, Kamada N (2020) Interleukin-22-mediated host glycosylation prevents Clostridioides difficile infection by modulating the metabolic activity of the gut microbiota. Nature Medicine 26(4): 608–617.

Kitamoto S, Alteri CJ, Rodrigues M, Nagao-Kitamoto H, Sugihara K, Himpsl SD, Bazzi M, Miyoshi M, Nishioka T, Hayashi A, Morhardt TL, Kuffa P, Grasberger H, El-Zaatari M, Bishu S, Ishii C, Hirayama A, Eaton KA, Dogan B, Simpson KW, Inohara N, Mobley HLT, Kao JY, Fukuda S, Barnich N, Kamada N (2020) Dietary L-serine confers a competitive fitness advantage to Enterobacteriaceae in the inflamed gut. Nature Microbiology 5(1): 116–125.


Yang J, Tsukimi T, Yoshikawa M, Suzuki K, Takeda T, Tomita M, Fukuda S (2019) Cutibacterium acnes (Propionibacterium acnes) 16S rRNA genotyping of microbial samples from possessions contributes to owner identification. mSystems 4(6): e00594-19.

Reviews and Books


Zhang X, Ishikawa D, Ohkusa T, Fukuda S, Nagahara A. (2022) Hot topics on fecal microbiota transplantation for the treatment of inflammatory bowel disease. Frontiers in Medicine 9: 1068567.


Anbutsu H, Fukatsu T (2020) Symbiosis for insect cuticle formation. In "Cellular Dialogues in the Holobiont" Edited by T. C. G. Bosch and M. G. Hadfield; Chapter 12, pp. 201-216, CRC Press, Boca Raton.

Horinouchi T, Furusawa C (2020) Understanding metabolic adaptation by using bacterial laboratory evolution and trans-omics analysis. Biophysical Reviews 12: 677-682.

Furusawa C, Irie N (2020) Toward understanding of evolutionary constraints: experimental and theoretical approaches. Biophysical Reviews 12: 1155–1161.