Cited by 225Gut microbiota and healthAutism Spectrum Disorder ResearchGastrointestinal motility and disorders

The Gut Microbiota and Dysbiosis in Autism Spectrum Disorders

Open access
Hughes, Heather K., Rose, Destanie, Ashwood, Paul·2018·Current Neurology and Neuroscience Reports

Abstract

Purpose of ReviewThere is a growing body of evidence indicating the gut microbiota influence neurodevelopment and behavior. The purposes of this review are to provide an overview of studies analyzing the microbiota and their metabolites in autism spectrum disorders (ASD) and to discuss the possible mechanisms of action involved in microbial influence on the brain and behavior.Recent FindingsThe microbiota-gut-brain (MGB) axis has been extensively studied in animal models, and it is clear that alterations in the composition of microbiota alter neurological and behavioral outcomes. However, findings in human studies are less abundant. Although there are several studies so far showing altered microbiota (dysbiosis) in ASD, the results are heterogeneous and often contradictory. Intervention studies such as fecal microbiota transplant therapies show promise and lend credence to the involvement of the microbiota in ASD.SummaryA role for the microbiota in ASD is likely; however, further studies elucidating microbial or metabolomic signatures and mechanisms of action are needed. Future research should focus on intervention studies that can identify specific metabolites and immune mediators that improve with treatment to help identify etiologies and pathological mechanisms of ASD.

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Written from the paper’s full text.

TL;DR

This review synthesizes evidence that gut microbiota and dysbiosis are associated with autism spectrum disorders (ASD), with animal models supporting microbial influence on neurodevelopment and behavior while human findings remain heterogeneous and often contradictory. Intervention studies such as vancomycin and fecal microbiota transplant show promise, but causality and mechanisms remain unresolved.

Key findings

  • Animal models show that microbiota alterations affect behavior and neurodevelopment: germ-free rodents have altered stress responses, anxiety, exploratory behavior, and working memory; maternal immune activation (MIA) model ASD-like behaviors improve after *Bacteroides fragilis* treatment and depend on microbiota-induced T helper 17/IL-17 responses.
  • Human ASD studies report dysbiosis but no consensus: a meta-analysis of 15 studies could not amalgamate the often contradictory results; some studies found increased diversity, others decreased diversity/richness, and some no difference. Specific findings include increased *Clostridia*, *Desulfovibrio*, *Sutterella*, and *Ruminococcus torques*, and reduced *Bifidobacteria* and *Akkermansia muciniphila*; one study of 40 ASD (36 severe) and 40 typically developing children found decreased *Alistipes*, *Bilophila*, *Dialister*, *Parabacteroides*, and *Veillonella* but increased *Collinsella*, *Corynebacterium*, *Dorea*, and *Lactobacillus*.
  • Microbial metabolites are altered in ASD: elevated 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), p-cresol, 4-ethylphenylsulfate (4EPS), and quinolinic acid; altered short-chain fatty acids; and changes in tryptophan/kynurenine/serotonin pathways.
  • Intervention findings: oral vancomycin in 11 children with regressive ASD and diarrhea led to significantly improved social behavior and communication in 8 (~73%), but improvements reverted after treatment; fecal microbiota transplant in 18 ASD children improved GI symptoms and ASD-relevant behaviors, with increases in *Bifidobacterium*, *Prevotella*, and *Desulfovibrio* persisting at 8-week follow-up. Fungal studies found *Candida* in nearly 60% of ASD samples versus none in controls in one study, and *Candida* as the most abundant mycobiota at nearly twice the rate of typically developing children in another.

Methods

  • Design: narrative review of studies analyzing the microbiota and their metabolites in ASD and discussing possible mechanisms of microbial influence on the brain and behavior.
  • Data/sample: animal models (germ-free, MIA, BTBR, Shank3 knockout) and human studies in children with ASD, including stool, intestinal biopsy, duodenal samples, and urine/stool/blood metabolomics; Tables 1 and 2 summarize microbiota and metabolomics studies. No primary data collection is reported.
  • Main analysis: qualitative synthesis of the literature; no formal meta-analysis is performed, and the review notes that a prior meta-analysis of 15 studies could not amalgamate contradictory results.

Limitations

  • The paper states that human findings are heterogeneous and often contradictory, that a meta-analysis of 15 studies could not amalgamate results, and that tissue/specimen type and sample site, use of sibling controls, differing sequencing techniques, heterogeneity in age and sex, and diet/feeding problems may reduce comparability across studies.
  • The paper states that it is unknown whether GI dysfunction and dysbiosis are sequelae of ASD or directly contribute to causing ASD, and that further studies elucidating microbial or metabolomic signatures and mechanisms of action are needed.
  • Evident from the text: this is a narrative review rather than a systematic review, with no described formal search strategy, risk-of-bias assessment, or quantitative synthesis; many cited human studies are small pilot or preliminary studies.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1007/s11910-018-0887-6

Cites

113 of 113 references verified0 citation errors · 0 not checkable

Statistics

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Claims the paper makes

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  • Interpretationreasoning

    A role for the microbiota in ASD is likely.

    “A role for the microbiota in ASD is likely; however, further studies elucidating microbial or metabolomic signatures and mechanisms of action are needed.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Findings from animal models about microbiota-gut-brain mechanisms can be generalized to human ASD.
    • Rests on an assumption: Observed dysbiosis in ASD is functionally relevant to ASD rather than solely a consequence of diet, GI dysfunction, or other confounders.
  • Premisenone given

    The gut microbiota influence neurodevelopment and behavior.

    “There is a growing body of evidence indicating the gut microbiota influence neurodevelopment and behavior.”
    Quote in the paperNot a substantial claim
  • Premisecitation

    Reductions in Bifidobacteria and Akkermansia muciniphila have been shown in ASD.

    “As well as increases in some species, reductions in important commensals Bifidobacteria and the mucin-degrading Akkermansia muciniphila [52] have been shown in ASD.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [52] Wang L, Christophersen CT, Sorich MJ, Gerber JP, Angley MT, Conlon MA. Low relative abundances of the mucolytic bacterium Akkermansia muciniphila and Bifidobacterium spp. in feces of children with autism. Appl Environ Microbiol. 2011;77(18):6718–21. source

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  • Premisecitation

    There is some evidence that altering the microbiota in ASD can improve behaviors.

    “In addition to immune and GI dysfunction that may be linked to dysbiosis, there is some evidence that altering the microbiota in ASD can improve behaviors [46, 79•].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [46, 79•]

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  • Premisecitation

    Ileal and cecal biopsies from children with ASD and GI dysfunction showed increased Firmicutes and decreased Bacteroidetes.

    “Ileal and cecal biopsies from children with ASD and GI dysfunction showed increased Firmicutes and decreased Bacteroidetes [51].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [51] Williams BL, Hornig M, Buie T, Bauman ML, Cho Paik M, Wick I, et al. Impaired carbohydrate digestion and transport and mucosal dysbiosis in the intestines of children with autism and gastrointestinal disturbances. PLoS One. 2011;6(9):e24585. source

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  • May combine two claims. 41
  • Classified as probably not a substantial claim. 5
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    Premisecitation

    Immune dysfunction and gastrointestinal inflammation are common in individuals with ASD and contribute to severity of behaviors seen in the disorder.

    “Immune dysfunction and gastrointestinal (GI) inflammation are also common in individuals with ASD and contribute to severity of behaviors seen in the disorder [6–8].”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [6] Onore C, Careaga M, Ashwood P. The role of immune dysfunction in the pathophysiology of autism. Brain Behav Immun. 2012;26(3):383–92. source

      Not checked in the free run.

    • cites [7] McElhanon BO, McCracken C, Karpen S, Sharp WG. Gastrointestinal symptoms in autism spectrum disorder: a meta-analysis. Pediatrics. 2014;133(5):872–83. source

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    • cites [8] Mead J, Ashwood P. Evidence supporting an altered immune response in ASD. Immunol Lett. 2015;163(1):49–55. source

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  • May combine two claims.

    Premisenone given

    Intervention studies such as fecal microbiota transplant therapies show promise and lend credence to the involvement of the microbiota in ASD.

    “Intervention studies such as fecal microbiota transplant therapies show promise and lend credence to the involvement of the microbiota in ASD.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Premisenone given

    The microbiota-gut-brain axis has been extensively studied in animal models, and alterations in microbiota composition alter neurological and behavioral outcomes.

    “The microbiota-gut-brain (MGB) axis has been extensively studied in animal models, and it is clear that alterations in the composition of microbiota alter neurological and behavioral outcomes.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisenone given

    Several human studies show altered microbiota (dysbiosis) in ASD, but the results are heterogeneous and often contradictory.

    “Although there are several studies so far showing altered microbiota (dysbiosis) in ASD, the results are heterogeneous and often contradictory.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    Germ-free mice experience immune dysfunction and are more susceptible to infections than mice kept in conventional facilities.

    “These mice experience immune dysfunction and are more susceptible to infections than mice kept in conventional facilities [13, 15].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [13] Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121–41. source

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    • cites [15] Round JL, Mazmanian SK. The gut microbiome shapes intestinal immune responses during health and disease. Nature reviews. Immunology 2009;9(5):313–323. source

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    Premisecitation

    Increased Desulfovibrio and Bacteroides vulgatus were identified in children with ASD and were correlated to autism severity.

    “Increased Desulfovibrio and Bacteroides vulgatus were identified in children with ASD and were correlated to autism severity [50].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [50] Finegold SM, Dowd SE, Gontcharova V, Liu C, Henley KE, Wolcott RD, et al. Pyrosequencing study of fecal microflora of autistic and control children. Anaerobe. 2010;16(4):444–53. source

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    Interpretationcitation

    Disrupted barrier function could facilitate translocation of bacterial metabolites and immune mediators from the gut into circulation, which could lead to activation of microglia as seen in an induced dysbiosis mouse model.

    “disrupted barrier function could facilitate the translocation of bacterial metabolites and immune mediators from the gut into circulation (Fig. 1), which could lead to activation of microglia as seen in an induced dysbiosis mouse model [40].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [40] Bruce-Keller AJ, Salbaum JM, Luo M. Blanchard et, Taylor CM, welsh DA, et al. obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol Psychiatry. 2015;77(7):607–15. source

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    Premisecitation

    Deficits in germ-free mice can be corrected by colonization with diverse commensal bacteria, but this is age-dependent, suggesting composition and timing of colonization are critical for immune education.

    “These deficits can be corrected by colonization with diverse commensal bacteria; however, this has been shown to be age-dependent, suggesting that both composition and timing of colonization are critical for the education of the immune system [16–18].”
    Quote in the paperNot a substantial claim0 of 3 sources checked
    • cites [16] Chung H, Pamp SJ, Hill JA, Surana NK, Edelman SM, Troy EB, et al. Gut immune maturation depends on colonization with a host-specific microbiota. Cell. 2012;149(7):1578–93. source

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    • cites [17] El Aidy S, Hooiveld G, Tremaroli V, Backhed F, Kleerebezem M. The gut microbiota and mucosal homeostasis: colonized at birth or at adulthood, does it matter? Gut Microbes 2013;4(2):118–124. source

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    • cites [18] Gensollen T, Iyer SS, Kasper DL, Blumberg RS. How colonization by microbiota in early life shapes the immune system. Science. 2016;352(6285):539–44. source

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    Premisecitation

    The maternal immune activation model is dependent on microbiota that can induce a T helper 17 response; dams lacking certain microbiota could not mount this response, and their offspring did not display ASD-like behaviors.

    “Recently, this model has been shown to be dependent on microbiota that can induce a T helper (TH-) 17 response—dams that lacked certain microbiota could not mount this response, and their offspring did not display the ASD-like behaviors [42•, 43••].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [42•, 43••]

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    Premisecitation

    Microbiota produce neuroactive metabolites including GABA by Lactobacillus and Bifidobacteria, acetylcholine by Lactobacillus, dopamine by Bacillus and Serratia, and norepinephrine by Escherichia and Saccharomyces, which could enter circulation and directly affect neural processes including the brain.

    “Microbiota produce other neuroactive metabolites including GABA by Lactobacillus and Bifidobacteria [36], acetylcholine by Lactobacillus, dopamine by Bacillus and Serratia, and norepinephrine by Escherichia and Saccharomyces, which could enter circulation and directly affect neural processes throughout the body, including the brain (Fig. 1) [37].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [37] Lyte M. Probiotics function mechanistically as delivery vehicles for neuroactive compounds: microbial endocrinology in the design and use of probiotics. BioEssays. 2011;33(8):574–81. source

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    Premisecitation

    Parracho et al. confirmed increased Clostridia in stool samples, and its presence highly correlated with GI symptoms in ASD children.

    “Using fluorescence in situ hybridization (FISH) techniques to identify bacteria present in stool samples, Parracho et al. confirmed increased Clostridia, and its presence highly correlated with GI symptoms in ASD children [49].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [49] Parracho HM, Bingham MO, Gibson GR, McCartney AL. Differences between the gut microflora of children with autistic spectrum disorders and that of healthy children. J Med Microbiol. 2005;54(Pt 10):987–91. source

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  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Premisecitation

    The gut microbiota play a critical role in the development of the intestinal architecture and mucosal immune system and are important for regulation of the immune system in the gut.

    “The gut microbiota play a critical role in the development of the intestinal architecture and mucosal immune system and are particularly important for regulation of the immune system in the gut [reviewed in [13, 14]].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [13] Belkaid Y, Hand TW. Role of the microbiota in immunity and inflammation. Cell. 2014;157(1):121–41. source

      Not checked in the free run.

    • cites [14] Hooper LV, Littman DR, Macpherson AJ. Interactions between the microbiota and the immune system. Science. 2012;336(6086):1268–73. source

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    Premisecitation

    Dysbiosis introduced in conventionally housed adult mice leads to abnormal behaviors, altered barrier functions, and activation of microglia.

    “In addition, dysbiosis introduced in conventionally housed adult mice also leads to abnormal behaviors, altered barrier functions, and activation of the microglia, the resident immune cells of the brain [40].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [40] Bruce-Keller AJ, Salbaum JM, Luo M. Blanchard et, Taylor CM, welsh DA, et al. obese-type gut microbiota induce neurobehavioral changes in the absence of obesity. Biol Psychiatry. 2015;77(7):607–15. source

      Not checked in the free run.

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    Premisecitation

    Stress in early life can induce dysbiosis and influence immune responses, as shown in maternal separation models of stress.

    “Conversely, stress in early life can induce dysbiosis and influence immune responses, as shown in maternal separation models of stress [32].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [32] O'Mahony SM, Marchesi JR, Scully P, Codling C, Ceolho AM, Quigley EM, et al. Early life stress alters behavior, immunity, and microbiota in rats: implications for irritable bowel syndrome and psychiatric illnesses. Biol Psychiatry. 2009;65(3):263–7. source

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    Premisecitation

    In Shank3 knockout mice, differences were seen specifically in males, with significant alterations in GABA receptor gene expression that could be modulated with Lactobacillus reuteri.

    “The latter study saw differences specifically in males, with significant alterations in GABA receptor gene expression in the Shank3 KO mice that could be modulated with the introduction of the probiotic Lactobacillus reuteri [45].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [45] Tabouy L, Getselter D, Ziv O, Karpuj M, Tabouy T, Lukic I, et al. Dysbiosis of microbiome and probiotic treatment in a genetic model of autism spectrum disorders. In: Brain Behav Immun; 2018.

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    Premisecitation

    The gut microbiota can influence brain function and lead to changes in behaviors, as shown extensively in animal models.

    “The gut microbiota can influence brain function and lead to changes in behaviors, as shown extensively in animal models [22•].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [22•]

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    Premisecitation

    Dysbiosis and impaired intestinal barrier function were seen in a maternal immune activation model of autism, with improvements in ASD-relevant behavior after treatment with Bacteroides fragilis.

    “Dysbiosis and impaired intestinal barrier function were seen in a maternal immune activation (MIA) model of autism, with improvements in ASD relevant behavior after treatment with Bacteriodes fragilis [41].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [41] Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;155(7):1451–63. source

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  • May combine two claims.

    Premisecitation

    In germ-free mice, the architecture of the mesenteric lymph nodes and Peyer's patches is smaller and disorganized, with reduced maturation of isolated lymphoid follicles and fewer immune cells.

    “In germ-free (GF) mice, the architecture of the mesenteric lymph nodes and Peyers patches is smaller and disorganized, with reduced maturation of isolated lymphoid follicles and fewer numbers of immune cells present.”
    Quote in the paperNot a substantial claim
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    Premisecitation

    One culture-based study showed significant presence of Candida species in the feces of children with ASD, the majority Candida albicans, and fluconazole-resistant species including C. krusei and C. glabrata were also found.

    “So far, fungal microbiota studies in ASD are scant; however, one culture-based study showed significant presence of Candida species in the feces of children with ASD, the majority of which were Candida albicans. Fluconozole-resistant species were also found in significant numbers of cultures, including C. krusei and C. glabrata [96].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [96] Kantarcioglu AS, Kiraz N, Aydin A. Microbiota-gut-brain Axis: yeast species isolated from stool samples of children with suspected or diagnosed autism Spectrum disorders and in vitro susceptibility against nystatin and fluconazole. Mycopathologia. 2016;181(1–2):1–7. source

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    Premisecitation

    A separate study found Candida present in nearly 60% of ASD samples, with none present in controls, and identified hyphae formation suggesting the yeast had switched to its invasive and adhesive form.

    “A separate study found Candida present in nearly 60% of ASD samples, with none present in controls. They also identified hyphae formation, suggesting that the dimorphic yeast had switched to its invasive and adhesive form [97].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [97] Iovene MR, Bombace F, Maresca R, Sapone A, Iardino P, Picardi A, et al. Intestinal Dysbiosis and yeast isolation in stool of subjects with autism Spectrum disorders. Mycopathologia. 2017;182(3–4):349–63. source

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    Premisecitation

    Children with ASD are known to have feeding problems, food sensitivities or aversions, and extremely restricted diets, which could contribute to differences in microbiota but not to an ASD diagnosis.

    “Children with ASD are known to have feeding problems, food sensitivities/aversions, and extremely restricted diets [89], which could also be contributing to differences in microbiota but not to an ASD diagnosis.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [89] Cermak SA, Curtin C, Bandini LG. Food selectivity and sensory sensitivity in children with autism spectrum disorders. J Am Diet Assoc. 2010;110(2):238–46. source

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    Premisecitation

    In animal models of ASD, elevations of microbial metabolite 4-ethylphenylsulfate correlated with altered behaviors in mice, and probiotic therapy reduced its concentration and improved behaviors in the MIA model.

    “In animal models of ASD, elevations of microbial metabolite 4-ethylphenylsulfate (4EPS) correlated with altered behaviors in mice, and probiotic therapy reduced its concentration and improved behaviors in MIA model of ASD [41].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [41] Hsiao EY, McBride SW, Hsien S, Sharon G, Hyde ER, McCue T, et al. Microbiota modulate behavioral and physiological abnormalities associated with neurodevelopmental disorders. Cell. 2013;155(7):1451–63. source

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    Premisecitation

    A preliminary study of 22 children with ASD and GI dysfunction found that D-arabinitol concentrations and D-arabinitol/L-arabinitol ratios were significantly reduced with daily probiotics, and improvements were seen in certain ASD behaviors including ability to concentrate.

    “A preliminary study of 22 children with ASD and GI dysfunction found that DA concentrations and DA/LA ratios were significantly reduced with daily administration of probiotics, and improvements were seen in certain ASD behaviors including ability to concentrate [62].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [62] Kaluzna-Czaplinska J, Blaszczyk S. The level of arabinitol in autistic children after probiotic therapy. Nutrition (Burbank, Los Angeles County, Calif) 2012;28(2):124–6. source

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    Premisecitation

    A large recent study of 40 ASD children (36 severe) and 40 typically developing controls found decreased abundance of Alistipes, Bilophila, Dialister, Parabacteroides, and Veillonella families but increased Collinsella, Corynebacterium, Dorea, and Lactobacillus.

    “One of the largest of recent studies that looked at 40 ASD (36 severe) and 40 typically developing control children found decreased abundance of the Alistipes, Bilophila, Dialister, Parabacteroides, and Veillonella families but increased Collinsella, Corynebacterium, Dorea, and Lactobacillus, suggesting major changes in the microbiota composition in ASD.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [78] Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, et al. New evidences on the altered gut microbiota in autism spectrum disorders. Microbiome. 2017;5(1):24. source

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    Interpretationcitation

    Immune activation may be responsible for the elevation of quinolinic acid in ASD, as activated macrophages and microglia are the main producers of quinolinic acid.

    “Immune activation may be responsible for this elevation, as activated macrophages and microglia are the main producers of QA [106].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [106] Guillemin GJ, Smith DG, Smythe GA, Armati PJ, Brew BJ. Expression of the kynurenine pathway enzymes in human microglia and macrophages. Adv Exp Med Biol. 2003;527:105–12. source

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    Premisecitation

    Increases in an alternative branch of the kynurenine pathway led to reduced kynurenic acid and elevated quinolinic acid, an excitotoxic NMDA receptor agonist, in children with ASD.

    “Increases in an alternative branch of the kynurenine pathway led to reduced kynurenic acid and elevated quinolinic acid (QA), a compound known to be an excitotoxic N-methyl-D-aspartate (NMDA) receptor agonist, in children with ASD [68] (Fig. 1).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [68] Gevi F, Zolla L, Gabriele S, Persico AM. Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism. Molecular Autism. 2016;7:47. source

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    Premisecitation

    Short-chain fatty acids influence gene expression epigenetically through histone deacetylase inhibition; butyrate-producing bacteria promote peripheral regulatory T cell expansion, altering gut immunity by promoting tolerance, through increased acetylation at the Foxp3 promoter and expansion of CD4+ Foxp3+ Tregs.

    “SCFA influence gene expression epigenetically through histone deacetylase (HDAC) inhibition. For example, butyrate-producing bacteria promote peripheral regulatory T cell (Tregs) expansion, altering gut immunity by promoting tolerance. This occurs through HDAC inhibition leading to increased acetylation at the Foxp3 promotor and expansion of CD4+ Foxp3+ Tregs [102••].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [102••]

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    Premisecitation

    The composition of microbiota is very sensitive to changes in diet, fiber composition, and other factors, and can also be altered by stress and other compounding factors.

    “Note that the composition of microbiota is very sensitive to changes diet, fiber composition, etc., and can also be altered by stress and other compounding factors [10].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [10] RodrÍguez JM, Murphy K, Stanton C, Ross RP, Kober OI, Juge N, et al. The composition of the gut microbiota throughout life, with an emphasis on early life. Microb Ecol Health Dis. 2015;26(1):26050.

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    Premisecitation

    Serotonin plays important neurotrophic roles during early development, and elevations of 5-HT during critical time periods can alter cognition and sensory processing.

    “Serotonin plays important neurotrophic roles during early development, and elevations of 5-HT during critical time periods can alter cognition and sensory processing [109].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [109] Miceli S, Negwer M, van Eijs F, Kalkhoven C, van Lierop I, Homberg J, et al. High serotonin levels during brain development alter the structural input-output connectivity of neural networks in the rat somatosensory layer IV. Front Cell Neurosci. 2013;7:88. source

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    Premisecitation

    Altered patterns of bacterial metabolites were seen in a large number of children with ASD compared to healthy controls, including elevated HPHPA, a catabolic byproduct of Clostridia.

    “Altered patterns of bacterial metabolites were seen in a large number of children with ASD compared to healthy control children. These metabolites included elevated 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), a catabolic byproduct of Clostridia [59].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [59] Shaw W. Increased urinary excretion of a 3-(3-hydroxyphenyl)-3-hydroxypropionic acid (HPHPA), an abnormal phenylalanine metabolite of clostridia spp. in the gastrointestinal tract, in urine samples from patients with autism and schizophrenia. Nutr Neurosci. 2010;13(3):135–43. source

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    Premisecitation

    Metabolome studies have repeatedly shown evidence of alterations in tryptophan, kynurenine, and serotonin pathways in children with ASD, including increased urinary excretion of tryptophan and associated metabolites.

    “Metabolome studies have repeatedly shown evidence of alterations in tryptophan, kynurenine, and serotonin pathways in children with ASD, including reports of increased urinary excretion of tryptophan and associated metabolites [63, 67, 68, 72, 105].”
    Quote in the paperSubstantial claim0 of 5 sources checked
    • cites [63] Ming X, Stein TP, Barnes V, Rhodes N, Guo L. Metabolic perturbance in autism spectrum disorders: a metabolomics study. J Proteome Res. 2012;11(12):5856–62. source

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    • cites [67] Noto A, Fanos V, Barberini L, Grapov D, Fattuoni C, Zaffanello M, et al. The urinary metabolomics profile of an Italian autistic children population and their unaffected siblings. J Matern Fetal Neonatal Med. 2014;27(sup2):46–52. source

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    • cites [68] Gevi F, Zolla L, Gabriele S, Persico AM. Urinary metabolomics of young Italian autistic children supports abnormal tryptophan and purine metabolism. Molecular Autism. 2016;7:47. source

      Not checked in the free run.

    • cites [72] Lussu M, Noto A, Masili A, Rinaldi AC, Dessì A, De Angelis M, et al. The urinary 1H-NMR metabolomics profile of an italian autistic children population and their unaffected siblings. Autism Res. 2017;10(6):1058–66. source

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    • cites [105] Diémé B, Mavel S, Blasco H, Tripi G, Bonnet-Brilhault F, Malvy J, et al. Metabolomics study of urine in autism Spectrum disorders using a multiplatform analytical methodology. J Proteome Res. 2015;14(12):5273–82. source

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  • May combine two claims.

    Premisecitation

    Several studies found lower levels of fecal short-chain fatty acids, including butyrate, in feces of ASD children, while a 2012 study found increased ammonia and short-chain fatty acids including acetic, butyric, isobutyric, valeric, and isovaleric acids in ASD.

    “Several studies found lower levels of fecal SCFA, including butyrate in feces of ASD children [53, 64], while a 2012 study found increased ammonia and SCFA including acetic, butyric, isobutyric, valeric, and isovaleric acids in ASD [61].”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [53] Adams JB, Johansen LJ, Powell LD, Quig D, Rubin RA. Gastrointestinal flora and gastrointestinal status in children with autism--comparisons to typical children and correlation with autism severity. BMC Gastroenterol. 2011;11:22. source

      Not checked in the free run.

    • cites [64] De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI. Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One 2013;8. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    The majority of the fibers of the vagus nerve are afferent sensory fibers, delivering sensory information from the periphery, including the GI tract, to the brain.

    “The majority of the fibers of the vagus nerve are afferent sensory fibers, delivering sensory information from the periphery, including the GI tract, to the brain [110].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [110] Bonaz B, Bazin T, Pellissier S. The Vagus nerve at the Interface of the microbiota-gut-brain Axis. Front Neurosci. 2018;12:49. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Some short-chain fatty acids such as propionic acid can be neurotoxic in higher concentrations and have been shown to cause behavioral abnormalities in rodent models.

    “some SCFAs such as propionic acid (PPA) can be neurotoxic in higher concentrations and have been shown to cause behavioral abnormalities in rodent models [100, 101]”
    Quote in the paperSubstantial claim0 of 2 sources checked
    • cites [100] Shultz SR, MacFabe DF, Ossenkopp KP, Scratch S, Whelan J, Taylor R, et al. Intracerebroventricular injection of propionic acid, an enteric bacterial metabolic end-product, impairs social behavior in the rat: implications for an animal model of autism. Neuropharmacology. 2008;54(6):901–11. source

      Not checked in the free run.

    • cites [101] MacFabe DF, Cain NE, Boon F, Ossenkopp KP, Cain DP. Effects of the enteric bacterial metabolic product propionic acid on object-directed behavior, social behavior, cognition, and neuroinflammation in adolescent rats: relevance to autism spectrum disorder. Behav Brain Res. 2011;217(1):47–54. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Neural communication between the brain and the microbiota may occur through direct pattern recognition sensing due to Toll-like receptor expression on afferent fibers.

    “It is understood that neural communication between the brain and the microbiota may be occurring indirectly through hormones or neurotransmitter release by gut endocrine cells in presence of the microbiota and metabolites, or perhaps through direct pattern recognition sensing due to Toll-like receptor expression on afferent fibers [110].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [110] Bonaz B, Bazin T, Pellissier S. The Vagus nerve at the Interface of the microbiota-gut-brain Axis. Front Neurosci. 2018;12:49. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    Some studies found increased diversity of microbiota in ASD, whereas other studies show decreased diversity and richness or no differences in diversity.

    “Some studies found increased diversity of the microbiota in ASD [47, 64], whereas other studies show the opposite trend towards decreased diversity and richness [73, 74], or no differences in diversity [75, 77].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [47] Finegold SM, Molitoris D, Song Y, Liu C, Vaisanen ML, Bolte E, et al. Gastrointestinal microflora studies in late-onset autism. Clin Infect Dis. 2002;35(Suppl 1):S6–s16. source

      Not checked in the free run.

    • cites [64] De Angelis M, Piccolo M, Vannini L, Siragusa S, De Giacomo A, Serrazzanetti DI. Fecal microbiota and metabolome of children with autism and pervasive developmental disorder not otherwise specified. PLoS One 2013;8. source

      Not checked in the free run.

  • May combine two claims.

    Premisereasoning

    The gut microbiota are critical for regulating tryptophan metabolism, either directly by degrading tryptophan to indole derivatives or indirectly through mammalian kynurenine and serotonin pathways.

    “The gut microbiota are critical for regulating Trp metabolism, either directly by degrading Trp to indole-derivatives or indirectly through mammalian kynurenine and serotonin pathways.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    Germ-free mouse models have shown that the serotonergic system in the brain is influenced by the microbiota, whereby excess peripheral tryptophan may cross the blood-brain barrier to influence the rate of serotonin synthesis in the brain.

    “GF mouse models have shown that the serotonergic system in the brain is also influenced by the microbiota [24, 26], whereby excess peripheral Trp may cross the BBB to influence the rate serotonin synthesis in the brain [108].”
    Quote in the paperNot a substantial claim0 of 2 sources checked
    • cites [24] Neufeld KM, Kang N, Bienenstock J, Foster JA. Reduced anxiety-like behavior and central neurochemical change in germ-free mice. Neurogastroenterol Motil. 2011;23(3):255–64 e119. source

      Not checked in the free run.

    • cites [26] Clarke G, Grenham S, Scully P, Fitzgerald P, Moloney RD, Shanahan F, et al. The microbiome-gut-brain axis during early life regulates the hippocampal serotonergic system in a sex-dependent manner. Mol Psychiatry. 2013;18(6):666–73. source

      Not checked in the free run.

  • May combine two claims.

    Interpretationreasoning

    Shifts in short-chain fatty acid production could potentially contribute to altered immune regulation in the gut and lead to peripheral inflammation.

    “Therefore, shifts in SCFA production could potentially contribute to altered immune regulation in the gut and lead to peripheral inflammation (Fig. 1).”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Premisecitation

    There is no consensus for differences in microbiota in ASD, and a meta-analysis of 15 studies could not amalgamate the often contradictory results.

    “Overall, there does not seem to be consensus for differences in microbiota in ASD, and a meta-analysis of 15 studies could not amalgamate the often contradictory results [87].”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [87] Cao X, Lin P, Jiang P, Li C. Characteristics of the gastrointestinal microbiome in children with autism spectrum disorder: a systematic review. Shanghai Arch Psychiatry. 2013;25(6):342–53.

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    P-cresol, a microbial metabolite produced by Clostridium species, was significantly elevated in children with ASD, especially females with severe autism.

    “P-cresol, another microbial metabolite produced by Clostridium species, was significantly elevated in children with ASD, especially females with severe autism [60].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [60] Altieri L, Neri C, Sacco R, Curatolo P, Benvenuto A, Muratori F, et al. Urinary p-cresol is elevated in small children with severe autism spectrum disorder. Biomarkers: biochemical indicators of exposure, response, and susceptibility to chemicals. Biomarkers 2011;16(3):252–60. source

      Not checked in the free run.

  • May combine two claims.

    Premisecitation

    A recent clinical trial involving fecal microbiota transplant in 18 ASD children led to significantly improved GI symptoms and ASD-relevant behaviors, with increases in Bifidobacterium, Prevotella, and Desulfovibrio, and these changes persisted at the 8-week follow-up.

    “A recent clinical trial which involved fecal microbiota transplant (FMT) in 18 ASD children led to significantly improved GI symptoms and ASD-relevant behaviors, with increases in Bifidobacterium, Prevotella, and Desulfovibrio. These changes persisted at the 8-week follow-up [79•].”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [79•]

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S1 (asserted). May combine two claims.

    Interpretationreasoning

    Dysbiotic microbiota, their influence on the immune system, and their metabolic byproducts contribute directly to the development of these disorders.

    “Reports that behaviors improve after modification of the microbiota support the hypothesis that dysbiotic microbiota, their influence on the immune system, and their metabolic byproducts contribute directly to the development of these disorders.”
    Quote in the paperNot a substantial claim
43 of 43
  • The paper relies on this without support.

    Findings from animal models about microbiota-gut-brain mechanisms can be generalized to human ASD.

    “Through such animal studies, evidence is mounting that dysbiosis or altered microbiota composition has an impact on neurodevelopment and behavior.”
  • The paper relies on this without support.

    Observed dysbiosis in ASD is functionally relevant to ASD rather than solely a consequence of diet, GI dysfunction, or other confounders.

    “The studies discussed in this review have identified significant dysbiosis in children with ASD; however, it is unknown whether the GI dysfunction and dysbiosis is sequelae of the larger disorder or whether they directly contribute to causing ASD.”
  • The paper relies on this without support.

    Microbiota profiles from stool or biopsy specimens represent the gut microbial community relevant to brain and behavior.

    “Tissue/specimen type and sample site may account for the differences in studies.”
  • The paper relies on this without support.

    Immune system dysfunction is a well-known issue in ASD.

    “Immune system dysfunction is a well-known issue in ASD, possibly driving the dysbiotic microbiota, or alternatively created by it.”
4 of 4

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • The microbiota composition differs significantly between healthy controls and patients affected by neurodegenerative disorders such as multiple sclerosis, Alzheimer's and Parkinson's diseases, and neuropsychiatric disorders.

    “The microbiota composition differs significantly between healthy controls and patients affected by neurodegenerative disorders (such as multiple sclerosis (MS), Alzheimer’s (AD) and Parkinson’s (PD) diseases) (20, 22, 23, 32, 111–115), and neuropsychiatric disorders (NPS) (30), like major depressive and mood disorders.”

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Authors
Hughes, H. K., Rose, D., & Ashwood, P.
Affiliations
University of California, Davis (US)
Corresponding author
Ashwood, Paul
Venue
Current Neurology and Neuroscience Reports
Published
2018-09-24
Volume
18
Issue
11
Pages
81-81
ISSN
  • 1528-4042 (ISSN-L)
  • 1534-6293
OpenAlex
W2892751773
Cited by
225
References
113
Citations by year
2026: 10 · 2025: 26 · 2024: 34 · 2023: 25 · 2022: 50 · 2021: 35 · 2020: 28 · 2019: 15 · 2018: 2
FWCI
1.96
Type
journal article
Language
en
Open access
Locations
  • Current Neurology and Neuroscience Reports (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (acceptedVersion)
  • eScholarship (California Digital Library) (submittedVersion)
Funders
  • National Science Foundation (1650042)
  • Autism Speaks
  • Autism Research Institute
  • National Alliance for Research on Schizophrenia and Depression
  • National Institute of Environmental Health Sciences (R01ES015359, ES011269, P01ES011269, R829388, R21ES025560, R833292)
  • National Center for Research Resources (UL1RR024146)
  • Eunice Kennedy Shriver National Institute of Child Health and Human Development (R21HD086669, U54HD079125, R01HD090214)
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
gut microbiota, dysbiosis, autism spectrum disorder, microbiota-gut-brain axis, microbial metabolites, fecal microbiota transplantation, brain development, behavior, immune mediators, metabolomic signatures
MeSH terms
Autism Spectrum Disorder, Gastrointestinal Microbiome, Animals, Brain, Humans, Metabolomics, Microbiota, Dysbiosis

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.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-09.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-09.

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