Metagenomic Characterization of Gut Microbiota in Children with Autism Spectrum Disorder: Microbial Signatures and Modulation by Anti-Inflammatory Diet and Probiotics
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Study information
-
Quality control
- Retracted paper
- Contamination issues suspected
- Batch effect issues suspected
- Uncontrolled confounding suspected
- Results are suspect (various reasons)
- Tags applied
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI Uniform resource identifier for web resources.
Authors
Valencia-Buitrago M., Oliveira-Carvalho R.D., Cardoso V., Triviño-Valencia J., Salamanca-Duque L.M., Martínez-Díaz V., Zabaleta J., Galeano-Vanegas N.F., Naranjo-Galvis C.A.
Journal
Pharmaceuticals (Basel, Switzerland)
Year
2025
Keywords:
Colombian children, anti-inflammatory diet, autism spectrum disorder, gastrointestinal disorders, gut microbiota, metagenomics, probiotics
Background: Autism Spectrum Disorder (ASD) is increasingly associated with alterations in gut microbiota, intestinal permeability, and immune dysregulation. However, integrative studies exploring these mechanisms in Latin American populations are lacking. Objective: To characterize gut microbiota profiles in Colombian children with ASD and evaluate the effects of two microbiota-targeted interventions, an anti-inflammatory diet and a probiotic formulation, on microbial diversity and taxonomic composition. Methods: In a two-phase study, shotgun metagenomic sequencing was performed on fecal samples from 23 children with ASD and 7 typically developing (TD) controls. In the second phase, 17 children with ASD were randomized to receive a 12-week intervention (anti-inflammatory diet, probiotics, or no intervention). Alpha diversity indices (Shannon, Pielou, and Chao1) and differential abundance analyses were conducted. Results: Compared to TD children, those with ASD showed a higher Firmicutes/Bacteroidetes ratio and a significantly increased abundance of genera such as Clostridioides, Thomasclavelia, Alistipes, and Coprococcus. The presence of functional gastrointestinal disorders (FGIDs) in ASD patients is associated with reduced microbial richness. POST-intervention, the anti-inflammatory diet group showed that no statistically significant changes in alpha diversity were observed, although a slight upward trend was noted and significant enrichment of six bacterial genera, including Moraxella and Eubacterium. The probiotic group exhibited a significant increase in Romboutsia and a decrease in Lachnospira. Cytokine-microbiota networks in ASD were fragmented and dominated by IFN-γ and MCP-1 hubs, indicating systemic immune activation. Interventions induced functional remodeling: The anti-inflammatory diet increased the number of beneficial genera (Eubacterium, Adlercreutzia) and shifted networks toward positive correlations involving IL-8 and MIP-1β. Probiotics increased Romboutsia, reduced Lachnospira, and restructured networks with regulatory cytokines (SDF-1α, Eotaxin) and SCFA-producing taxa (Blautia, Roseburia). Conclusions: Children with ASD in Colombia displayed distinct microbial profiles characterized by pro-inflammatory taxa and altered richness. Both the anti-inflammatory diet and probiotics produced compositional shifts in the gut microbiota, although global changes in diversity were limited. These findings support the potential of microbiota-targeted nutritional strategies for ASD and underscore the need for precision interventions tailored to specific clinical and microbial phenotypes.
Experiment 1
Needs review
Subjects
- Location of subjects
- Colombia
- Host species Species from which microbiome was sampled. Contact us to have more species added.
- Homo sapiens
- Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology
- Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Autism spectrum disorder atypical autism,autism spectrum disease,autism spectrum disorder,Autism Spectrum Disorders,autistic spectrum disorder,CHILD DEVELOPMENT DIS PERVASIVE,Child Development Disorders, Pervasive,Development Disorder, Pervasive,Development Disorders, Pervasive,Disorder, Autism Spectrum,Disorder, Pervasive Development,Disorders, Autism Spectrum,Disorders, Pervasive Development,PDD,PERVASIVE CHILD DEVELOPMENT DIS,Pervasive Child Development Disorders,Pervasive Development Disorder,Pervasive Development Disorders,pervasive developmental disorder - not otherwise specified,pervasive developmental disorders,Spectrum Disorder, Autism,Spectrum Disorders, Autism,Autism spectrum disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- Typically Developing (TD)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- Autism Spectrum Disorder (ASD)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed clinical diagnosis of Autism Spectrum Disorder (ASD) based on the criteria established by pediatric neurology or child psychiatry professionals in accordance with the national clinical protocol for ASD diagnosis and care (MinSalud, 2015) and classified as High-Functioning Autism (Level I, DSM-5).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 23
- Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)
- 3 months
Lab analysis
- Sequencing type
- WMS
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- Not specified
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Illumina
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- Welch's T-Test
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.05
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- Yes
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 4
Description: Genera found to be significantly more abundant in fecal samples of children with ASD compared to typically developing (TD) controls (Welch's t-test, Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: increased abundance in Autism Spectrum Disorder (ASD)
| NCBI | Quality Control | Links |
|---|---|---|
| Clostridioides | ||
| Thomasclavelia | ||
| Alistipes | ||
| Hungatella | ||
| Coprococcus | ||
| Sarcina | ||
| Monoglobus |
Revision editor(s): Amara-Chikaodili
Experiment 2
Needs review
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TD without FGIDs
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ASD without FGIDs
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Confirmed ASD (Level I, DSM-5) diagnosis without Functional Gastrointestinal Disorders (FGIDs).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 8
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "None" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.None
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "None" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.None
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 6
Description: Genera found to be significantly more abundant in fecal samples of children with ASD without FGIDs compared to typically developing (TD) controls without FGIDs (Welch's t-test, Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: increased abundance in ASD without FGIDs
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Alistipes |
Revision editor(s): Amara-Chikaodili
Experiment 3
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Diet Dietary,Diets,Diet,diet
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ASD Diet PRE-intervention
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ASD Diet POST-intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- A Specific anti-inflammatory dietary protocol, designated as "NeuroGutPlus," which was formulated using regionally accessible, polyphenol-rich, and fiber-dense foods, administered over a 12-week intervention period to children with ASD (Level I, DSM-5).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 5
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Matched on Factors on which subjects have been matched on in a case-control study
- Matched on: "none" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.none
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 12
Description: Genera with significantly increased relative abundance (Welch's t-test) in ASD children POST-intervention compared to PRE-intervention after 12 weeks of an anti-inflammatory diet (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: increased abundance in ASD Diet POST-intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Adlercreutzia | ||
| Altererythrobacter | ||
| Eubacterium | ||
| Moraxella | ||
| Novisyntrophococcus | ||
| Sellimonas |
Revision editor(s): Amara-Chikaodili
Experiment 4
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Therapeutic Procedure Therapeutic Procedure,therapeutic Procedure
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- ASD Probiotics PRE-intervention
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ASD Probiotics POST-intervention
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- Participants had a confirmed clinical diagnosis of high-functioning Autism Spectrum Disorder (Level I, DSM-5). The Therapeutic Procedure involved the administration of a multi-strain probiotic formulation over a 12-week intervention period to modulate the gut microbiota.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 6
- Group 1 sample size Number of subjects in the case (exposed) group
- 6
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "none" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.none
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 13
Description: Genera with significantly altered relative abundance (Welch's t-test) in ASD children POST-intervention compared to PRE-intervention after 12 weeks of probiotic supplementation (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: increased abundance in ASD Probiotics POST-intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Altererythrobacter | ||
| Moraxella | ||
| Romboutsia |
Revision editor(s): Amara-Chikaodili
Signature 2
Needs review
Source: Figure 13
Description: Genera with significantly altered relative abundance (Welch's t-test) in ASD children POST-intervention compared to PRE-intervention after 12 weeks of probiotic supplementation (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: decreased abundance in ASD Probiotics POST-intervention
| NCBI | Quality Control | Links |
|---|---|---|
| Lachnospira |
Revision editor(s): Amara-Chikaodili
Experiment 6
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Functional abnormality of the gastrointestinal tract Functional abnormality of the GI tract,GI dysfunction,Functional abnormality of the gastrointestinal tract,functional abnormality of the gastrointestinal tract
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TD (No FGIDs)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- TD (FGIDs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The presence of Functional Gastrointestinal Disorders (FGIDs), which are disorders of gut-brain interaction. This comparison contrasts TD children with FGIDs (Group 1) against TD children without FGIDs (Group 0) to assess the impact of GI symptomatology on the microbial community in a neurotypical population.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 3
- Group 1 sample size Number of subjects in the case (exposed) group
- 4
Lab analysis
Statistical Analysis
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 7
Description: Genera showing significantly altered relative abundance (Welch's t-test) in Typically Developing children with FGIDs compared to those without FGIDs. Both genera were more abundant in the TD group without FGIDs (Group 0), reflecting depletion of beneficial taxa associated with GI symptomatology (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: decreased abundance in TD (FGIDs)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum | ||
| Coprococcus |
Revision editor(s): Amara-Chikaodili
Experiment 7
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Autism spectrum disorder , Functional abnormality of the gastrointestinal tract atypical autism,autism spectrum disease,autism spectrum disorder,Autism Spectrum Disorders,autistic spectrum disorder,CHILD DEVELOPMENT DIS PERVASIVE,Child Development Disorders, Pervasive,Development Disorder, Pervasive,Development Disorders, Pervasive,Disorder, Autism Spectrum,Disorder, Pervasive Development,Disorders, Autism Spectrum,Disorders, Pervasive Development,PDD,PERVASIVE CHILD DEVELOPMENT DIS,Pervasive Child Development Disorders,Pervasive Development Disorder,Pervasive Development Disorders,pervasive developmental disorder - not otherwise specified,pervasive developmental disorders,Spectrum Disorder, Autism,Spectrum Disorders, Autism,Autism spectrum disorder,Functional abnormality of the GI tract,GI dysfunction,Functional abnormality of the gastrointestinal tract,functional abnormality of the gastrointestinal tract
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TD (Overall)
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- ASD (FGIDs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The coexistence of Autism Spectrum Disorder (ASD), defined by clinical diagnosis (Level I, DSM-5), and the presence of Functional Gastrointestinal Disorders (FGIDs).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 7
- Group 1 sample size Number of subjects in the case (exposed) group
- 15
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "None" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.None
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- decreased
Signature 1
Needs review
Source: Figure 8
Description: Genera with significantly altered relative abundance (Welch's t-test) in ASD children with FGIDs compared to the overall TD control group (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: increased abundance in ASD (FGIDs)
| NCBI | Quality Control | Links |
|---|---|---|
| Parabacteroides | ||
| Bacteroides | ||
| Alistipes | ||
| Akkermansia | ||
| Phascolarctobacterium |
Revision editor(s): Amara-Chikaodili
Signature 2
Needs review
Source: Figure 8
Description: Genera with significantly altered relative abundance (Welch's t-test) in ASD children with FGIDs compared to the overall TD control group (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: decreased abundance in ASD (FGIDs)
| NCBI | Quality Control | Links |
|---|---|---|
| Prevotella |
Revision editor(s): Amara-Chikaodili
Experiment 8
Needs review
Differences from previous experiment shown
Subjects
- Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology
- Autism spectrum disorder atypical autism,autism spectrum disease,autism spectrum disorder,Autism Spectrum Disorders,autistic spectrum disorder,CHILD DEVELOPMENT DIS PERVASIVE,Child Development Disorders, Pervasive,Development Disorder, Pervasive,Development Disorders, Pervasive,Disorder, Autism Spectrum,Disorder, Pervasive Development,Disorders, Autism Spectrum,Disorders, Pervasive Development,PDD,PERVASIVE CHILD DEVELOPMENT DIS,Pervasive Child Development Disorders,Pervasive Development Disorder,Pervasive Development Disorders,pervasive developmental disorder - not otherwise specified,pervasive developmental disorders,Spectrum Disorder, Autism,Spectrum Disorders, Autism,Autism spectrum disorder
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- TD (FGIDs)
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- The coexistence of Autism Spectrum Disorder (ASD), defined by a confirmed clinical diagnosis of high-functioning Autism Spectrum Disorder (Level I, DSM-5), and Functional Gastrointestinal Disorders (FGIDs). This experiment specifically compares this group (Group 1) against Typically Developing children who also have FGIDs (Group 0).
- Group 0 sample size Number of subjects in the control (unexposed) group
- 4
Lab analysis
Statistical Analysis
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- Confounders controlled for: "none" is not in the list (abnormal glucose tolerance, acetaldehyde, acute graft vs. host disease, acute lymphoblastic leukemia, acute myeloid leukemia, adenoma, age, AIDS, alcohol consumption measurement, alcohol drinking, ...) of allowed values.none
Alpha Diversity
- Pielou Quantifies how equal the community is numerically
- unchanged
- Shannon Estimator of species richness and species evenness: more weight on species richness
- unchanged
- Chao1 Abundance-based estimator of species richness
- unchanged
Signature 1
Needs review
Source: Figure 9
Description: Genera with significantly altered relative abundance (Welch's t-test) in ASD children with FGIDs compared to TD children with FGIDs. All listed genera were increased in the ASD FGIDs group (Benjamini-Hochberg FDR p<0.05).
Abundance in Group 1: increased abundance in ASD (FGIDs)
| NCBI | Quality Control | Links |
|---|---|---|
| Anaerobutyricum | ||
| Clostridioides | ||
| Coprococcus | ||
| Enterocloster | ||
| Hungatella | ||
| Klebsiella | ||
| Lachnoclostridium | ||
| Thomasclavelia |
Revision editor(s): Amara-Chikaodili
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