New evidences on the altered gut microbiota in autism spectrum disorders

From BugSigDB
Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021
study design
case-control
Citation
PMID
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
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 16 July 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743, Rimsha

Subjects

Location of subjects Country from which study subjects were recruited
Italy
Host species Species from which microbiome was sampled (if applicable)
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
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
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 Experimental technique used for quantifying microbial abundance
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

Statistical test Statistical test or computational tool used for differential abundance testing
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 9 February 2021

Curated date: 2019-02-21

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

Source: Figure 2

Description: Mean relative abundance in autistic (AD) and neurotypical (NT) subjects

Abundance in Group 1: decreased abundance in autistic

NCBI Links
Bacteroidota

Revision editor(s): WikiWorks743

Experiment 2


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
Italy
Host species Species from which microbiome was sampled (if applicable)
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
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
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 Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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


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 9 February 2021

Curated date: 2019-02-21

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

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 Links
Lactobacillus
Collinsella
Corynebacterium
Corynebacteriaceae
Dorea
Bacteroidia

Revision editor(s): WikiWorks743

Signature 2

Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021

Curated date: 2019-02-21

Curator: Fatima Zohra

Revision editor(s): WikiWorks743

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 Links
Alistipes
Veillonellaceae
Selenomonadales
Negativicutes
Dialister
Parabacteroides
Veillonella
Bilophila
Bacteroidales

Revision editor(s): WikiWorks743

Experiment 3


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
Italy
Host species Species from which microbiome was sampled (if applicable)
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
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
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 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
29
Group 1 sample size Number of subjects in the case (exposed) group
5
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 Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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


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 9 February 2021

Curated date: 2019-11-08

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks743

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 Links
Escherichia
Shigella
Clostridium

Revision editor(s): WikiWorks743

Experiment 4


Reviewed Marked as Reviewed by Shaimaa Elsafoury on 9 February 2021

Curated date: 2021/01/10

Curator: WikiWorks743

Revision editor(s): WikiWorks753, WikiWorks743

Subjects

Location of subjects Country from which study subjects were recruited
Italy
Host species Species from which microbiome was sampled (if applicable)
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
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
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 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
29
Group 1 sample size Number of subjects in the case (exposed) group
11
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 Experimental technique used for quantifying microbial abundance
16S
Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance
Roche454

Statistical Analysis

Statistical test Statistical test or computational tool used for differential abundance testing
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


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 9 February 2021

Curated date: 2019-11-08

Curator: Shaimaa Elsafoury

Revision editor(s): WikiWorks743

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 Links
Gemmiger

Revision editor(s): WikiWorks743