A preliminary investigation on the relationship between gut microbiota and gene expressions in peripheral mononuclear cells of infants with autism spectrum disorders

QIIME allows analysis of high-throughput community sequencing data

Caporaso, J. G., Kuczynski, J., Stombaugh, J., Bittinger, K., Bushman, F. D., Costello, E. K., Fierer, N., Peña, A. G., Goodrich, J. K., Gordon, J. I., et al. (2010) · Nature Methods · doi:10.1038/nmeth.f.303 · Cited by 34,887

Search and clustering orders of magnitude faster than BLAST

Edgar, R. C. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq461 · Cited by 21,098

Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy

Wang, Q., Garrity, G. M., Tiedje, J. M., & Cole, J. R. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.00062-07 · Cited by 20,145

FLASH: fast length adjustment of short reads to improve genome assemblies

Magoč, T., & Salzberg, S. L. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr507 · Cited by 15,366

UCHIME improves sensitivity and speed of chimera detection

Edgar, R. C., Haas, B. J., Clemente, J. C., Quince, C., & Knight, R. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr381 · Cited by 15,114

Mechanisms of type-I- and type-II-interferon-mediated signalling

Platanias, L. C. (2005) · Nature reviews. Immunology · doi:10.1038/nri1604 · Cited by 3,631

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

Hsiao, E. Y., McBride, S. W., Hsien, S., Sharon, G., Hyde, E. R., McCue, T., Codelli, J. A., Chow, J., Reisman, S. E., Petrosino, J. F., et al. (2013) · Cell · doi:10.1016/j.cell.2013.11.024 · Cited by 3,283

Human nutrition, the gut microbiome and the immune system

Kau, A. L., Ahern, P. P., Griffin, N. W., Goodman, A. L., & Gordon, J. I. (2011) · Nature · doi:10.1038/nature10213 · Cited by 2,588

Autism

Lai, M.-C., Lombardo, M. V., & Baron-Cohen, S. (2014) · The Lancet · doi:10.1016/s0140-6736(13)61539-1 · Cited by 2,371

Neuroglial activation and neuroinflammation in the brain of patients with autism

Vargas, D. L., Nascimbene, C., Krishnan, C., Zimmerman, A. W., & Pardo, C. A. (2005) · Annals of Neurology · doi:10.1002/ana.20315 · Cited by 2,149

Gut microbiota maturation and early behavioral and cognitive development

Zhu, Z., Yang, Y., Samuel, T. M., Li, T., Yin, W., Howell, B., Cho, S., Hazlett, H. C., Elison, J. T., Hongtu Zhu, B., et al. (2025) · Scientific Reports · doi:10.1038/s41598-025-13530-1 · Cited by 4

Dietary supplementation with 1‐kestose induces altered locomotor activity and increased striatal dopamine levels with a change in gut microbiota in male mice

Altaisaikhan, A., Yoshihara, K., Hata, T., Miyata, N., Asano, Y., Suematsu, T., Kadota, Y., & Sudo, N. (2023) · Physiological Reports · doi:10.14814/phy2.15882 · Cited by 3

Dysregulated metabolism and behaviors by disrupting gut microbiota in prenatal and neonatal mice

Han, G., Nishigawa, T., Ikeda, H., Hamada, M., Yang, H., Maesono, S., Aso, K., Jing, A., Furuse, M., & Zhang, R. (2021) · Animal Science Journal · doi:10.1111/asj.13566 · Cited by 4

Gut-brain axis and immunoneuroendocrine modulation in neurological and psychiatric disorders: A systematic review

Lami, K. F., de Oliveira, V. F., & Batista, K. Z. S. (2021) · Research Society and Development · doi:10.33448/rsd-v10i4.14185 · Cited by 4

Microbial dysbiosis as a diagnostic marker in psychiatric disorders: a systematic review of gut–brain axis disruptions

Villagomez, P. E., Hinojosa-Figueroa, M. S., Vallejo, P., Pérez, F., Burneo, G., Villarreal, C., Rodas, J. A., & León-Rojas, J. E. (2026) · Frontiers in Neuroscience · doi:10.3389/fnins.2026.1728473 · Cited by 6

Associations between the gut microbiota at one-year and neurodevelopment in children from the SEPAGES cohort

Davias, A., Lyon-Caen, S., Iszatt, N., Monot, C., Rayah, Y., Ilhan, Z. E., Guichardet, K., Bayat, S., Valmary‐Degano, S., Muckle, G., et al. (2025) · Brain Behavior & Immunity - Health · doi:10.1016/j.bbih.2025.101063 · Cited by 5

In silico analysis of autism spectrum disorder through the integration of DNA methylation and gene expression data for biomarker search

Sevimoğlu, T. (2023) · Minerva Biotechnology and Biomolecular Research · doi:10.23736/s2724-542x.23.02956-5 · Cited by 3

Identification of target hub genes and construction of a novel miRNA regulatory network in autism spectrum disorder by integrated analysis

Zhu, J., Meng, H., & Li, Y. (2023) · Medicine · doi:10.1097/md.0000000000034420 · Cited by 3

Comparison of the fecal bacterial microbiota in mice, rats, and pigs after oral administration of alpha-glycosyl isoquercitrin

Liu, H., Inoue, R., Koyanagi, M., Hayashi, S., Watanabe, G., & Nagaoka, K. (2024) · The Journal of Toxicological Sciences · doi:10.2131/jts.49.151 · Cited by 3

The Impacts of Probiotics on Microbiota in Patients With Autism Spectrum Disorder

Chen, H.-J., & Liu, Y.-W. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-819265-8.00101-7 · Cited by 3

Intestinal D-amino acids content is highly related to intestinal IgA production upon soluble dietary fiber ingestion in mice

Matsumoto, K., Noguchi, A., Miyamoto, F., Inoue, R., Hirai, H., Miwa, T., Nakagawa, Y., & Higashimura, Y. (2025) · Food Chemistry · doi:10.1016/j.foodchem.2025.144719 · Cited by 2

EFFECTS OF CLOSTRIDIUM BUTYRICUM SUPPLEMENTATION ON FECAL MICROBIOTA AND METABOLITES IN CAPTIVE RED KANGAROO (MACROPUS RUFUS)

Yoshimoto, Y., Ichinohe, N., Liu, H., Nagata, N., Inoüe, R., Yamamoto, Y., & Nagaoka, K. (2025) · Journal of Zoo and Wildlife Medicine · doi:10.1638/2024-0079 · Cited by 2

Bacterial community of the shrimp (Litopenaeus vannamei) gut and its relationship with water quality in a recirculating aquaculture system (RAS)

Emmanuel, A., Raza, B., Ramzan, M. N., & Zheng, Z. (2025) · Aquaculture International · doi:10.1007/s10499-025-02349-2 · Cited by 2

L-amino acid oxidase-1 is involved in the gut-liver axis by regulating 5-aminolevulinic acid production in mice

Qasimi, M. I., Fukuzawa, S., Suenaga, K., Kambe, J., Li, C., Tomonaga, S., Kawase, T., Tsukahara, T., Hirayama, K., INOUE, R., et al. (2023) · Journal of Veterinary Medical Science · doi:10.1292/jvms.23-0080 · Cited by 2

Dietary Supplementation of Vitamin B12 to Rats Fed High-Amylose Cornstarch Normalizes Propionate Fermentation in the Colon

UMEDA, T., YAMADA, C., Kawase, T., Tsukahara, T., INOUE, R., Hino, S., & Nishimura, N. (2024) · Journal of Nutritional Science and Vitaminology · doi:10.3177/jnsv.70.139 · Cited by 2

Metataxonomic and Immunological Analysis of Feces from Children with or without Phelan–McDermid Syndrome

Alba, C., Herranz, C., Monroy, M. A., Aragón, A., Jurado, R., Díaz‐Regañón, D., Sánchez, C., Tolín, M., Miranda, C., Gómez-Taylor, B., et al. (2024) · Microorganisms · doi:10.3390/microorganisms12102006 · Cited by 2

Altered gut–brain signaling in autism spectrum disorders—from biomarkers to possible intervention strategies

Sauer, A. K., Dooley, L., Vaughan, A., & Grabrucker, A. M. (2021) · Elsevier eBooks · doi:10.1016/b978-0-12-822822-7.00007-7 · Cited by 2

Metabolic and Microbial Characterizations for the Gastrointestinal Digesta of the Zoo Colobus guereza

Toyoda, A., Shionome, N., Kohari, D., Iida, S., Hitachi Kamine Zoo, J., Masato, H., 4Hitachi Kamine Zoo, J., Namae, N., 4Hitachi Kamine Zoo, J., Nakamura, S., et al. (2021) · Journal of Bacteriology and Mycology · doi:10.26420/jbacteriolmycol.2021.1162 · Cited by 2

Temporal effects of lascufloxacin on human gut and salivary microbiota: Analysis using next-generation sequencing method

Mukuda, K., Inoüe, R., Takata, M., Takazawa, K., Noma, H., Morishima, S., Oda, M., Ma’arif, A. S., Endo, Y., Sunada, H., et al. (2024) · Journal of Infection and Chemotherapy · doi:10.1016/j.jiac.2024.07.023 · Cited by 1

Heyndrickxia coagulans SANK70258 supplementation improves growth performance, gut health, and liver function in growing pigs

Aida, M., Yamada, R., Kawase, T., Matsuo, T., & Tsukahara, T. (2025) · Frontiers in Veterinary Science · doi:10.3389/fvets.2025.1537913 · Cited by 1

Enhancing Quercetin Bioavailability Attenuates Aging Phenotypes via the Gut Microbiota–Intestinal Barrier Axis in Aged Mice

Naito, Y., Mizushima, K., Inoue, R., & Takagi, T. (2026) · Nutrients · doi:10.3390/nu18101537 · Cited by 1

Screening and Bioinformatics Analysis of Differential Genes in Autism Spectrum Disorder Based on GEO Database

Zhu, J., Meng, H., & Li, Y. (2023) · Studies in health technology and informatics · doi:10.3233/shti230851 · Cited by 1

Effects of Zinc Supplementation in the Elderly with Focus on Muscle Mass, Dry Skin, and Gut Microbiota

Nakagawa, N., Enokiya, T., Tochitani, S., Nakahigashi, M., Nishida, K., Ooi, K., Kawanishi, S., & Toyoda, N. (2023) · BPB Reports · doi:10.1248/bpbreports.6.6_217 · Cited by 1

Associations Between the Microbiome and Neurocognitive and Neuropsychiatric Function

Lundwall, R. A. (2024) · Oxford University Press eBooks · doi:10.1093/oso/9780192870414.003.0024 · Cited by 1

Characterization of the gut phageome of Japanese patients with ulcerative colitis under endoscopic remission

Otsuki, A., Inoüe, R., Imai, T., Miura, H., Nishida, A., Inatomi, O., & Andoh, A. (2024) · Journal of Clinical Biochemistry and Nutrition · doi:10.3164/jcbn.24-173 · Cited by 1

ALTERAÇÕES NA MICROBIOTA GASTROINTESTINAL DE CRIANÇAS COM TRANSTORNO DO ESPECTRO AUTISTA: UMA REVISÃO SISTEMÁTICA

Martins, F. D. N. P., Cunha, L. B. G., & Lacerda, E. M. D. C. B. (2021) · Psicologia e Saúde em Debate · doi:10.22289/2446-922x.v7n2a11 · Cited by 1

Influence of Amino Acids on Autism and Attention-Deficit Hyperactive Disorder

Begum, P. S., Razak, M. A., & Rajagopal, S. (2022) · Nutritional neurosciences · doi:10.1007/978-981-15-9781-7_10 · Cited by 1

Effect of gum arabic supplementation on in vitro fermentation with ruminal fluid from high forage-fed animals

Matsui, H., Tsukahara, T., ARAKI, T., HOTTA, Y., & Takagi, T. (2022) · Nihon Chikusan Gakkaiho · doi:10.2508/chikusan.93.105

Nutrition’s Route to Behaviour and Vice Versa: Longitudinal Links from Early Life to Adolescence

Willemsen, Y. (2024) · Radboud University Press eBooks · doi:10.54195/9789493296374

Additional file 3 of Metagenomics revealed a correlation of gut phageome with autism spectrum disorder

Shahin, K., Soleimani-Delfan, A., He, Z., Sansonetti, P. J., & Collard, J. (2023) · Figshare · doi:10.6084/m9.figshare.23884303

Additional file 1 of Metagenomics revealed a correlation of gut phageome with autism spectrum disorder

Shahin, K., Soleimani-Delfan, A., He, Z., Sansonetti, P. J., & Collard, J. (2023) · Figshare · doi:10.6084/m9.figshare.23884297

Additional file 2 of Metagenomics revealed a correlation of gut phageome with autism spectrum disorder

Shahin, K., Soleimani-Delfan, A., He, Z., Sansonetti, P. J., & Collard, J. (2023) · Figshare · doi:10.6084/m9.figshare.23884300

Additional file 4 of Metagenomics revealed a correlation of gut phageome with autism spectrum disorder

Shahin, K., Soleimani-Delfan, A., He, Z., Sansonetti, P. J., & Collard, J. (2023) · Figshare · doi:10.6084/m9.figshare.23884306

Additional file 5 of Metagenomics revealed a correlation of gut phageome with autism spectrum disorder

Shahin, K., Soleimani-Delfan, A., He, Z., Sansonetti, P. J., & Collard, J. (2023) · Figshare · doi:10.6084/m9.figshare.23884309

A Comprehensive Review of Medicinal Herbs Improving Gut-Brain Health

Ramanathan, A., Rani, K. R. V., Bhupathyraaj, M., Sridhar, S. B., Shareef, J., & Thomas, S. (2024) · Springer eBooks · doi:10.1007/978-981-19-3949-5_36-1 · Cited by 1

A pilot study: Examining cytoskeleton gene expression profiles in Pakistani children with autism spectrum disorder

Malik, S., Ali, S. A., Mehdi, A. M., Raza, A., Bashir, S., & Baig, D. N. (2024) · International Journal of Developmental Neuroscience · doi:10.1002/jdn.10372

A Comprehensive Review of Medicinal Herbs Improving Gut-Brain Health

Ramanathan, A., Rani, K. R. V., Bhupathyraaj, M., Sridhar, S. B., Shareef, J., & Thomas, S. (2024) · Springer eBooks · doi:10.1007/978-981-99-7557-0_36

Colonic Dysbiosis Is Associated with Gastrointestinal Disorders More than Mother–Child Epidemiological Traits in Mexican Children with Autism Spectrum Disorders

Herrera-Mejía, J., Wall‐Medrano, A., Ramos‐Jiménez, A., González-Córdova, A. F., Jiménez-Vega, F., & Campos-Vega, R. (2025) · Gastroenterology Insights · doi:10.3390/gastroent16020015

Additional file 3 of Matcha green tea beverage moderates fatigue and supports resistance training-induced adaptation

Shigeta, M., Aoi, W., Morita, C., Soga, K., Inoue, R., Fukushima, Y., Kobayashi, Y., & Kuwahata, M. (2024) · Figshare · doi:10.6084/m9.figshare.26602099

Additional file 6 of Matcha green tea beverage moderates fatigue and supports resistance training-induced adaptation

Shigeta, M., Aoi, W., Morita, C., Soga, K., Inoue, R., Fukushima, Y., Kobayashi, Y., & Kuwahata, M. (2024) · Figshare · doi:10.6084/m9.figshare.26602108

Additional file 2 of Matcha green tea beverage moderates fatigue and supports resistance training-induced adaptation

Shigeta, M., Aoi, W., Morita, C., Soga, K., Inoue, R., Fukushima, Y., Kobayashi, Y., & Kuwahata, M. (2024) · Figshare · doi:10.6084/m9.figshare.26602096

Additional file 1 of Matcha green tea beverage moderates fatigue and supports resistance training-induced adaptation

Shigeta, M., Aoi, W., Morita, C., Soga, K., Inoue, R., Fukushima, Y., Kobayashi, Y., & Kuwahata, M. (2024) · Figshare · doi:10.6084/m9.figshare.26602090

Additional file 4 of Matcha green tea beverage moderates fatigue and supports resistance training-induced adaptation

Shigeta, M., Aoi, W., Morita, C., Soga, K., Inoue, R., Fukushima, Y., Kobayashi, Y., & Kuwahata, M. (2024) · Figshare · doi:10.6084/m9.figshare.26602102

Additional file 5 of Matcha green tea beverage moderates fatigue and supports resistance training-induced adaptation

Shigeta, M., Aoi, W., Morita, C., Soga, K., Inoue, R., Fukushima, Y., Kobayashi, Y., & Kuwahata, M. (2024) · Figshare · doi:10.6084/m9.figshare.26602105

Changes in the microbiome and metabolome in captive red kangaroos ( Osphranter rufus ) affected by macropod progressive periodontal disease

Yoshimoto, Y., Nagata, N., Inoüe, R., Yamamoto, Y., & Nagaoka, K. (2026) · Australian Veterinary Journal · doi:10.1111/avj.70057

Behavioral deficits, organ weight changes, and altered gut microbiota in single-housed middle-aged mice

Nishi, S., Yajima, Y., Shimoda, S., Isozaki, Y., Kawase, T., Tsukahara, T., & Toyoda, A. (2026) · Physiology & Behavior · doi:10.1016/j.physbeh.2026.115316

Effect of gut microbiota from children with autism spectrum disorder (ASD) on behavior and ASD-related biological markers in germ-free mice

Roussin, L. (2023) · theses.fr (ABES) · doi:10.70675/998d3bd1z4618z400dz998cz89e524b35aef · Cited by 1

Maillard reaction with milk proteins reduced the prebiotic activity of 2’-fucosyllactose in a neonatal rat model

Liu, S., Pan, Y., Tu, Y., Liu, X., Wu, C., Liu, J., Liu, M., Wang, C., Zhang, T., Ren, F., et al. (2026) · Food Chemistry · doi:10.1016/j.foodchem.2026.149410

Oral and Gut Microbiota in Individuals With Autism Spectrum Disorder: A Pilot Case–Control Study

Iida, A., Toyota, Y., Itagaki, T., Yawaka, Y., & Hasebe, A. (2026) · International Journal of Paediatric Dentistry · doi:10.1111/ipd.70095

The microbiota–gut–brain axis as a modulator of symptom expression in autism spectrum disorder, with exploratory insights into ADHD: evidence from a structured narrative review on paediatric population

Carta, A., Riccio, M. P., Miola, A., Cavassa, V., Puci, M. V., Abbracciavento, G., Carucci, S., Sambataro, F., Bravaccio, C., & Sotgiu, S. (2026) · Frontiers in Child and Adolescent Psychiatry · doi:10.3389/frcha.2026.1835043

Mucosa-associated gut microbiome in Japanese patients with functional constipation.

杉谷, 義., 稲富, 理., 西田, 淳., 今井, 隆., 河原, 真., 安藤, 朗., Sugitani, Y., INOUE, R., Inatomi, O., NISHIDA, A., et al. (2021) · Institutional Repositories DataBase (IRDB)

Maternal gut microbiota disruption alters postpartum maternal behavior in association with modulation of stress responses and brain tryptophan metabolism in mice

Tochitani, S., Yamamoto, Y., Saito, K., & Nagaoka, K. (2026) · Brain Behavior and Immunity · doi:10.1016/j.bbi.2026.106936

Relationship between fertility and hindgut microbiota of beef cows in pre- and postpartum periods

Katsumata, S., Tsukahara, T., Shindo, A., Sugiyama, S., Hirooka, H., Inoue, R., Saeki, K., & Kumagai, H. (2026) · animal · doi:10.1016/j.animal.2026.102006

Functional analysis of gut microbiota and immunoinflammation in children with autism spectrum disorders

Carissimi, C., Laudadio, I., Palone, F., Fulci, V., Cesi, V., Cardona, F., Alfonsi, C., Cucchiara, S., Isoldi, S., & Stronati, L. (2019) · Digestive and Liver Disease · doi:10.1016/j.dld.2019.06.006 · Cited by 62

Autism spectrum disorder is associated with gut microbiota disorder in children

Sun, H., You, Z., Jia, L., & Wang, F. (2019) · BMC Pediatrics · doi:10.1186/s12887-019-1896-6 · Cited by 53

Early-life differences in the gut microbiota composition and functionality of infants at elevated likelihood of developing autism spectrum disorder

Zuffa, S., Schimmel, P., Gonzalez-Santana, A., Belzer, C., Knol, J., Bölte, S., Falck‐Ytter, T., Forssberg, H., Swann, J. R., & Heijtz, R. D. (2023) · Translational Psychiatry · doi:10.1038/s41398-023-02556-6 · Cited by 79

Differential immune responses and microbiota profiles in children with autism spectrum disorders and co-morbid gastrointestinal symptoms

Rose, D. R., Yang, H., Serena, G., Sturgeon, C., Ma, B., Careaga, M., Hughes, H. K., Angkustsiri, K., Rose, M., Hertz-Picciotto, I., et al. (2018) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2018.03.025 · Cited by 227

Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study

Xu, X., Lang, J., Yang, J., Long, B., Liu, X., Zeng, X.-F., Tian, G., & You, X. (2023) · Frontiers in Immunology · doi:10.3389/fimmu.2023.1100816 · Cited by 12