New evidences on the altered gut microbiota in autism spectrum disorders
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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
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
URI
Authors
Strati F, Cavalieri D, Albanese D, De Felice C, Donati C, Hayek J, Jousson O, Leoncini S, Renzi D, Calabrò A, De Filippo C
Journal
Microbiome
Year
2017
Keywords:
Autism spectrum disorders, Constipation, Gut microbiota, Metataxonomy, Mycobiota
BACKGROUND: Autism spectrum disorders (ASDs) are neurodevelopmental conditions characterized by social and behavioural impairments. In addition to neurological symptoms, ASD subjects frequently suffer from gastrointestinal abnormalities, thus implying a role of the gut microbiota in ASD gastrointestinal pathophysiology. RESULTS: Here, we characterized the bacterial and fungal gut microbiota in a cohort of autistic individuals demonstrating the presence of an altered microbial community structure. A fraction of 90% of the autistic subjects were classified as severe ASDs. We found a significant increase in the Firmicutes/Bacteroidetes ratio in autistic subjects due to a reduction of the Bacteroidetes relative abundance. At the genus level, we observed a decrease in the relative abundance of Alistipes, Bilophila, Dialister, Parabacteroides, and Veillonella in the ASD cohort, while Collinsella, Corynebacterium, Dorea, and Lactobacillus were significantly increased. Constipation has been then associated with different bacterial patterns in autistic and neurotypical subjects, with constipated autistic individuals characterized by high levels of bacterial taxa belonging to Escherichia/Shigella and Clostridium cluster XVIII. We also observed that the relative abundance of the fungal genus Candida was more than double in the autistic than neurotypical subjects, yet due to a larger dispersion of values, this difference was only partially significant. CONCLUSIONS: The finding that, besides the bacterial gut microbiota, also the gut mycobiota contributes to the alteration of the intestinal microbial community structure in ASDs opens the possibility for new potential intervention strategies aimed at the relief of gastrointestinal symptoms in ASDs.
Experiment 1
Reviewed Marked as Reviewed by Fatima on 2021/07/16
Subjects
- Location of subjects
- Italy
- 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 autism,autism (disease),autism spectrum disorder,Autism, Early Infantile,Autism, Infantile,autism, susceptiblity to,Autisms,Autistic Disorder,autistic disorder,autistic disorder of childhood onset,Autistic disorder of childhood onset (disorder),childhood autism,Disorder, Autistic,Disorders, Autistic,Early Infantile Autism,Infantile Autism,infantile autism,Infantile autism (disorder),Infantile Autism, Early,Infantile psychosis (disorder),Kanner Syndrome,Kanner's Syndrome,Kanner's syndrome,Kanners Syndrome,Syndrome, Kanner's,Autism
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- neurotypical
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- autistic
- Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group
- cases were diagnosed according to the Diagnostic and Statistical Manual of Mental Disorders, 5th Edition.
- Group 0 sample size Number of subjects in the control (unexposed) group
- 40
- Group 1 sample size Number of subjects in the case (exposed) group
- 40
- 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
- 16S
- 16S variable region One or more hypervariable region(s) of the bacterial 16S gene
- V3-V5
- Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
- Roche454
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- raw counts
- 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
- Confounders controlled for Confounding factors that have been accounted for by stratification or model adjustment
- age, sex
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 2
Description: Mean relative abundance in autistic (AD) and neurotypical (NT) subjects
Abundance in Group 1: decreased abundance in autistic
| NCBI | Quality Control | Links |
|---|---|---|
| Bacteroidota |
Revision editor(s): WikiWorks
Experiment 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
Lab analysis
Statistical Analysis
- Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).
- relative abundances
- Statistical test
- LEfSe
- Significance threshold p-value or FDR threshold used for differential abundance testing (if any)
- 0.01
- MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?
- No
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- 2
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 3
Description: Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects
Abundance in Group 1: increased abundance in autistic
| NCBI | Quality Control | Links |
|---|---|---|
| Lactobacillus | ||
| Collinsella | ||
| Corynebacterium | ||
| Corynebacteriaceae | ||
| Dorea | ||
| Bacteroidia |
Revision editor(s): WikiWorks
Signature 2
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 3
Description: Differences in the bacterial taxa between autistic (AD) and neurotypical (NT) subjects
Abundance in Group 1: decreased abundance in autistic
| NCBI | Quality Control | Links |
|---|---|---|
| Alistipes | ||
| Veillonellaceae | ||
| Selenomonadales | ||
| Negativicutes | ||
| Dialister | ||
| Parabacteroides | ||
| Veillonella | ||
| Bilophila | ||
| Bacteroidales |
Revision editor(s): WikiWorks
Experiment 3
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non constipated autistic
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- constipated autistic
- Group 0 sample size Number of subjects in the control (unexposed) group
- 29
- Group 1 sample size Number of subjects in the case (exposed) group
- 5
Lab analysis
Statistical Analysis
- Statistical test
- Mann-Whitney (Wilcoxon)
- 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
- LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool
- Not specified
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 4
Description: Differences in the bacterial taxa between constipated and non-constipated autistic (AD) patients
Abundance in Group 1: increased abundance in constipated autistic
| NCBI | Quality Control | Links |
|---|---|---|
| Escherichia | ||
| Shigella | ||
| Clostridium |
Revision editor(s): WikiWorks
Experiment 4
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Differences from previous experiment shown
Subjects
- Group 0 name Corresponds to the control (unexposed) group for case-control studies
- non constipated neurotypical
- Group 1 name Corresponds to the case (exposed) group for case-control studies
- constipated neurotypical
- Group 1 sample size Number of subjects in the case (exposed) group
- 11
Lab analysis
Statistical Analysis
Signature 1
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 2021/02/09
Source: Figure 4
Description: Differences in the bacterial taxa between constipated and non-constipated neurotypical (NT) subjects
Abundance in Group 1: decreased abundance in constipated neurotypical
| NCBI | Quality Control | Links |
|---|---|---|
| Gemmiger |
Revision editor(s): WikiWorks
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