Gut Microbiota Features in Young Children With Autism Spectrum Disorders
Open accessAbstract
Proliferation and/or depletion of clusters of specific bacteria regulate intestinal functions and may interfere with neuro-immune communication and behavior in patients with autism spectrum disorder (ASD). Consistently, qualitative and quantitative alteration of bacterial metabolites may functionally affect ASD pathophysiology. Up to date, age-restricted cohort studies, that may potentially help to identify specific microbial signatures in ASD, are lacking. We investigated the gut microbiota (GM) structure and fecal short chain fatty acids (SCFAs) levels in a cohort of young children (2-4 years of age) with ASD, with respect to age-matched neurotypical healthy controls. Strong increase of Bacteroidetes and Proteobacteria and decrease of Actinobacteria was observed in these patients. Among the 91 OTUs whose relative abundance was altered in ASD patients, we observed a striking depletion of Bifidobacterium longum, one of the dominant bacteria in infant GM and, conversely, an increase of Faecalibacterium prausnitzii, a late colonizer of healthy human gut and a major butyrate producer. High levels of F. prausnitzii were associated to increase of fecal butyrate levels within normal range, and over representation of KEGG functions related to butyrate production in ASD patients. Here we report unbalance of GM structure with a shift in colonization by gut beneficial bacterial species in ASD patients as off early childhood.
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The prevalence of certain bacterial families, including Coriobacteriaceae, Actinomycetaceae, and Bifidobacteriaceae, has been observed to decline in individuals with ASD compared to the general population.
“Studies indicate that the prevalence of certain bacterial families, including Coriobacteriaceae, Actinomycetaceae, and Bifidobacteriaceae, has been observed to decline in individuals with ASD compared to those in the general population [8,101].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
Coretti et al. described a decrease in the populations of Corynebacterium and Actinomyces in individuals with ASD, while other authors have shown that the population of these bacteria should be elevated.
“Coretti et al. described a decrease in the populations of Corynebacterium and Actinomyces in individuals with ASD; nevertheless, other authors have shown that the population of these bacteria should be elevated [18,89,101,112].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
A multitude of scientific studies have reported a potential decrease in the abundance of Bifidobacterium in individuals diagnosed with ASD.
“A multitude of scientific studies have reported a potential decrease in the abundance of Bifidobacterium in individuals diagnosed with ASD [52,89,101,102,103,106,107,113].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
The abundance of the genus Faecalibacterium, particularly the species Faecalibacterium prausnitzii, should be lower in healthy individuals compared to patients diagnosed with ASD.
“It was also observed that the abundance of the genus Faecalibacterium, particularly the Faecalibacterium prausnitzii species, should be lower in healthy individuals compared to patients diagnosed with ASD [52,89,101,107,109,113].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
Coretti et al. and Ristori et al. suggest that, in patients diagnosed with ASD, there is not only an increase in the overall prevalence of Ruminococcus bacteria but also a potential elevation in the abundance of R. torques species.
“Furthermore, the research conducted by Coretti et al. and Ristori et al. suggests that, in patients diagnosed with ASD, there is not only an increase in the overall prevalence of Ruminococcus bacteria but also a potential elevation in the abundance of R. torques species [101,107].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
The results of various analyses indicate that the quantity of Oscillospira may be elevated or diminished in the guts of patients diagnosed with ASD.
“Furthermore, the results of various analyses indicate that the quantity of Oscillospira may be elevated or diminished in the guts of patients diagnosed with ASD [52,101,111,112].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
Ristori et al. revealed that individuals diagnosed with ASD exhibited a reduced population of bacteria from the Ruminococcus genus, while numerous studies have demonstrated that the population of these bacteria could be augmented.
“Ristori et al. revealed that individuals diagnosed with ASD exhibited a reduced population of bacteria from the Ruminococcus genus; however, numerous studies have demonstrated that the population of these bacteria could be augmented [101,107,109,110].”
From The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders (2025) · cites this paper as [101]
Gut bacterial communities differ between individuals with ASD and typically-developing controls.
“Gut bacterial communities differ between individuals with ASD and typically-developing (TD) controls (Coretti et al., 2018; De Angelis et al., 2013; Finegold et al., 2010; Gondalia et al., 2012; Kang et al., 2013, 2017a; Kushak et al., 2016; Liu et al., 2019; Son et al., 2015; Strati et al., 2017; Wang et al., 2019; Williams et al., 2011)”
From Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019) · cites this paper as Coretti et al., 2018
Microbiome profiles of ASD individuals, especially those with co-morbid GI dysfunction, differ from that of TD controls.
“Since then numerous studies from diverse cohorts have reported that microbiome profiles of ASD individuals, especially those with co-morbid GI dysfunction, differ from that of TD controls (Coretti et al., 2018; De Angelis et al., 2013; Finegold et al., 2010; Gondalia et al., 2012; Kang et al., 2013, 2017a; Kushak et al., 2016; Liu et al., 2019; Son et al., 2015; Strati et al., 2017; Wang et al., 2”
From Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice (2019) · cites this paper as Coretti et al., 2018
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Spichak, S., Bastiaanssen, T. F. S., Berding, K., Vlckova, K., Clarke, G., Dinan, T. G., & Cryan, J. F. (2021) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2021.02.044 · Cited by 127 · see citing works
Dargenio, V. N., Dargenio, C., Castellaneta, S., De Giacomo, A., Laguardia, M., Schettini, F., Francavilla, R., & Cristofori, F. (2023) · Nutrients · doi:10.3390/nu15071620 · Cited by 98 · see citing works
A Meta-analysis of Gut Microbiota in Children with Autism
Andreo-Martínez, P., Rubio-Aparicio, M., Sánchez-Meca, J., Veas, A., & Martínez-González, A. E. (2022) · Journal of Autism and Developmental Disorders · doi:10.1007/s10803-021-05002-y · Cited by 96 · see citing works
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Gut Microbiota and Autism Spectrum Disorder: A Neuroinflammatory Mediated Mechanism of Pathogenesis?
Zarimeidani, F., Rahmati, R., Mostafavi, M., Darvishi, M., Khodadadi, S., Mohammadi, M., Shamlou, F., Bakhtiyari, S., & Alipourfard, I. (2024) · Inflammation · doi:10.1007/s10753-024-02061-y · Cited by 47 · see citing works
The Many Faces of Microbiota-Gut-Brain Axis in Autism Spectrum Disorder
Gonçalves, C. L., Doifode, T., Rezende, V. L., Costa, M. A., Rhoads, J. M., & Soutullo, C. A. (2024) · Life Sciences · doi:10.1016/j.lfs.2023.122357 · Cited by 42 · see citing works
The Gut–Brain–Microbiota Connection and Its Role in Autism Spectrum Disorders
Młynarska, E., Barszcz, E., Budny, E., Gajewska, A., Kopeć, K., Wasiak, J., Rysz, J., & Franczyk, B. (2025) · Nutrients · doi:10.3390/nu17071135 · Cited by 44 · see citing works
Zheng, R., Huang, S., Feng, P., Liu, S., Jiang, M., Li, H., Zheng, P., Mi, Y., & Li, E. (2025) · Frontiers in Microbiology · doi:10.3389/fmicb.2025.1557174 · Cited by 6 · see citing works
Relationships between Gut Microbiota and Autism Spectrum Disorders: Development and Treatment
Poupard, L., Page, G., Thoreau, V., & Kaouah, Z. (2024) · Clinical Psychopharmacology and Neuroscience · doi:10.9758/cpn.24.1179 · Cited by 6 · see citing works
- Authors
- Coretti, L., Paparo, L., Riccio, M. P., Amato, F., Cuomo, M., Natale, A., Borrelli, L., Corrado, G., De Caro, C., Comegna, M., Buommino, E., Castaldo, G., Bravaccio, C., Chiariotti, L., Berni Canani, R., & Lembo, F.
- Affiliations
- University of Malta (MT)
- University of Naples Federico II (IT)
- Institute for Experimental Endocrinology and Oncology (IT)
- Corresponding author
- Coretti, Lorena
- Lembo, Francesca
- ORCID
- Venue
- Frontiers in Microbiology
- Publisher
- Frontiers Media SA
- Published
- 2018-12-19
- Volume
- 9
- Pages
- 3146-3146
- ISSN
- 1664-302X (ISSN-L)
- PMC
- PMC6305749
- OpenAlex
- W2904339023
- Cited by
- 266
- References
- 64
- Citations by year
- 2026: 29 · 2025: 34 · 2024: 41 · 2023: 27 · 2022: 36 · 2021: 57 · 2020: 30 · 2019: 11
- FWCI
- 8.71
- Type
- journal article
- Language
- en
- Update notices
- corrigendum (2019-05-03)
- Open access
- gold
- doi.org
- Licence
- Locations
- Frontiers in Microbiology (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
- Life Sciences › Neuroscience › Cognitive Neuroscience › Autism Spectrum Disorder Research
- Health Sciences › Medicine › Gastroenterology › Gastrointestinal motility and disorders
- Keywords
- autism spectrum disorder, gut microbiota, young children, short-chain fatty acids, butyrate, Faecalibacterium prausnitzii, Bifidobacterium longum, Bacteroidetes, Proteobacteria, actinobacteria, bacterial colonization, microbial signatures, neuroimmune interactions
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