. 2024 Mar 7;18:1341656. doi: 10.3389/fnins.2024.1341656

Table 4.

Evidence of microbiota alterations in Rett syndrome.

Study characteristics	Microbiota assessment	Increasing microbial taxa	Decreasing microbial taxa	Metabolites/Immune markers	Functional pathways
Strati et al. (2016) Cohort (CASP Score: 20) Sample size: N = 79 Age range (years): 5-26 Dietary habits: Not investigated GI symptoms: ↑constipation and inflammation (↑fecal calprotectin and ESR) in RETT	16S rRNA sequencing Fungal ITS1 rDNA region (Stool samples) Bacterial diversity Alpha diversity ↓bacterial richness (Shannon index) and species abundance (Chao1 index) RETT-C and RETT-NC Beta diversity RETT microbiota is different from NT No differences between RETT-C and RETT-NC ↑Firmicutes/Bacteroidetes ratio Fungal diversity Alpha diversity No differences Beta diversity RETT mycobiota is different from NT No differences between RETT-C and RETT-NC	Phylum (Bacteria) ↑Actinobacteria Genus (Bacteria) ↑Bifidobacterium Escherichia-Shigella Actinomyces Clostridium XIVa Anaerostipes Lactobacillus Blautia Eggerthella Enterococcus Erysipelotrichaceae incertae sedis Megasphaera Species (Bacteria) ↑Bifidobacterium longum Genus (Fungi) ↑Candida	Phylum (Bacteria) No decrease was observed Genus (Bacteria) ↓Bacteroides Faecalibacterium Gemmiger Ruminococcus Biophila Species (Bacteria) No decrease was observed Genus (Fungi) No decrease was observed	↑overall content of SCFAs (propionate, isovalerate/2-methylbutyrate, isobutyrate) in RETT Possible outcomes: Non-physiological high levels of SCFAs in the gut could contribute to the constipation status observed in RETT Non-physiological high levels of SCFAs affect gene expression, brain function and behavior, neurotransmitter systems, neuronal cell adhesion, inflammation, oxidative stress, lipid metabolism and mitochondrial function	↑carbohydrate and propanoate metabolism in the gut microbiota of RETT subjects (same pathways of SCFAs production) in RETT (PICRUSt-KEGG database)
Thapa et al. (2021) Case–control (CASP Score: 17) Sample size: N = 65 Age range (years): 5-36 Dietary habits: Documented and included in microbiota analysis GI symptoms: ↑GI symptoms in RETT	16S rRNA sequencing (Stool samples) Alpha diversity Between RETT and NT No differences Between RETT subgroups ↓in RETT pre-P vs. post-P ↓in RETT-severe vs. mild/moderate ↑in RETT solid food vs. formula Beta diversity Between RETT and NT No differences Between RETT subgroups Microbiota is different between: -RETT pre-P and post-P -RETT severe and mild/moderate -RETT food- and formula-fed	Genus ↑Bifidobacterium in RETT and NT formula-fed	Genus No decrease was observed	Microbial-derived metabolites: ↓fecal GABA and tyrosine concentrations in RETT compared to NT ↓fecal glutamate (not significant) in RETT compared to NT No changes in fecal tryptophan and glutamine between RETT and NT	Not investigated
Borghi et al. (2017) Case–control (CASP Score: 16) Sample size: N = 18 Age range (years): 15-30 Dietary habits: Documented; not included in the microbiota analysis GI symptoms: ↑constipation in RETT	16S rRNA sequencing (Stool samples) Alpha diversity ↓in RETT compared to NT ↓in RETT severe compared to mild/moderate (not significant) Beta diversity RETT microbiota is different from NT RETT severe is different from mild/moderate (not significant)	Between RETT and NT Family ↑Bacteroidaceae Genus ↑Bacteroides Species ↑Clostridium sp. Sutterella sp. Between RETT subgroups Family ↑Bacteroidaceae, Enterobacteriaceae Erysipelotrichaceae (In RETT mild compared to severe)	Between RETT and NT Family ↓Oscillospiraceae* Genus No decrease was observed Species ↓Faecalibacterium prasunitzii Prevotella sp. Roseburia sp. Between RETT subgroups Family ↓Oscillospiraceae (In RETT mild compared to severe)	Microbial-derived metabolites: No difference in total SCFAs and acetate between RETT and NT ↑Butyrate and propionate in RETT compared to NT ↑BCFAs in RETT compared to NT In RETT and NT: Positive correlation between: Parabacteroides and propionate, butyrate, and BCFA concentrations Alcaligenaceae and propionate Porphyromonadaceae and propionate, butyrate, and BCFA Ruminococcaceae and BMI Bacteroides and Clostridium and total protein and animal protein intake Negative correlation between: Bacteroidaceae, Bacteroides and total SCFAs and acetate Bacteroidaceae, Bacteroides, Veillonaceae and BMI	In RETT compared to NT ↓enzymes for carbohydrate and lipid metabolism ↑amino acids pathway ↑butanoate and propanoate metabolism (PICRUSt-KEGG database)

Study characteristics

Microbiota assessment

Increasing microbial taxa

Decreasing microbial taxa

Metabolites/Immune markers

Functional pathways

Strati et al. (2016)
Cohort (CASP Score: 20)
Sample size: N = 79
Age range (years): 5-26
Dietary habits:
Not investigated
GI symptoms:
↑constipation and inflammation (↑fecal calprotectin and ESR) in RETT

16S rRNA sequencing
Fungal ITS1 rDNA region
(Stool samples)
Bacterial diversity
Alpha diversity
↓bacterial richness (Shannon index) and species abundance (Chao1 index) RETT-C and RETT-NC
Beta diversity
RETT microbiota is different from NT
No differences between RETT-C and RETT-NC
↑Firmicutes/Bacteroidetes ratio
Fungal diversity
Alpha diversity
No differences
Beta diversity
RETT mycobiota is different from NT
No differences between RETT-C and RETT-NC

Phylum (Bacteria)
↑Actinobacteria
Genus (Bacteria)
↑Bifidobacterium
Escherichia-Shigella
Actinomyces
Clostridium XIVa Anaerostipes
Lactobacillus
Blautia
Eggerthella
Enterococcus
Erysipelotrichaceae incertae sedis
Megasphaera
Species (Bacteria)
↑Bifidobacterium longum
Genus (Fungi)
↑Candida

Phylum (Bacteria)
No decrease was observed
Genus (Bacteria)
↓Bacteroides
Faecalibacterium
Gemmiger
Ruminococcus
Biophila
Species (Bacteria)
No decrease was observed
Genus (Fungi)
No decrease was observed

↑overall content of SCFAs (propionate, isovalerate/2-methylbutyrate, isobutyrate) in RETT
Possible outcomes:
Non-physiological high levels of SCFAs in the gut could contribute to the constipation status observed in RETT
Non-physiological high levels of SCFAs affect gene expression, brain function and behavior, neurotransmitter systems, neuronal cell adhesion, inflammation, oxidative stress, lipid metabolism and mitochondrial function

↑carbohydrate and propanoate metabolism in the gut microbiota of RETT subjects (same pathways of SCFAs production) in RETT
(PICRUSt-KEGG database)

Thapa et al. (2021)
Case–control (CASP Score: 17)
Sample size: N = 65
Age range (years): 5-36
Dietary habits:
Documented and included in microbiota analysis
GI symptoms:
↑GI symptoms in RETT

16S rRNA sequencing
(Stool samples)
Alpha diversity
Between RETT and NT
No differences
Between RETT subgroups
↓in RETT pre-P vs. post-P
↓in RETT-severe vs. mild/moderate
↑in RETT solid food vs. formula
Beta diversity
Between RETT and NT
No differences
Between RETT subgroups
Microbiota is different between:
-RETT pre-P and post-P
-RETT severe and mild/moderate
-RETT food- and formula-fed

Genus
↑Bifidobacterium in RETT and NT formula-fed

Genus
No decrease was observed

Microbial-derived metabolites:
↓fecal GABA and tyrosine concentrations in RETT compared to NT
↓fecal glutamate (not significant) in RETT compared to NT
No changes in fecal tryptophan and glutamine between RETT and NT

Not investigated

Borghi et al. (2017)
Case–control (CASP Score: 16)
Sample size: N = 18
Age range (years): 15-30
Dietary habits:
Documented; not included in the microbiota analysis
GI symptoms:
↑constipation in RETT

16S rRNA sequencing
(Stool samples)
Alpha diversity
↓in RETT compared to NT
↓in RETT severe compared to mild/moderate
(not significant)
Beta diversity
RETT microbiota is different from NT
RETT severe is different from
mild/moderate
(not significant)

Between RETT and NT
Family
↑Bacteroidaceae
Genus
↑Bacteroides
Species
↑Clostridium sp.
Sutterella sp.
Between RETT subgroups
Family
↑Bacteroidaceae,
Enterobacteriaceae
Erysipelotrichaceae
(In RETT mild compared to severe)

Between RETT and NT
Family
↓Oscillospiraceae*
Genus
No decrease was observed
Species
↓Faecalibacterium prasunitzii
Prevotella sp.
Roseburia sp.
Between RETT subgroups
Family
↓Oscillospiraceae
(In RETT mild compared to severe)

Microbial-derived metabolites:
No difference in total SCFAs and acetate between RETT and NT
↑Butyrate and propionate in RETT compared to NT
↑BCFAs in RETT compared to NT
In RETT and NT:
Positive correlation between:

Parabacteroides and propionate, butyrate, and BCFA concentrations
Alcaligenaceae and propionate
Porphyromonadaceae and propionate, butyrate, and BCFA
Ruminococcaceae and BMI
Bacteroides and Clostridium and total protein and animal protein intake

Negative correlation between:

Bacteroidaceae, Bacteroides and total SCFAs and acetate
Bacteroidaceae, Bacteroides, Veillonaceae and BMI

In RETT compared to NT
↓enzymes for carbohydrate and lipid metabolism
↑amino acids pathway
↑butanoate and propanoate metabolism
(PICRUSt-KEGG database)

BCFA, branched chain fatty acids; BMI, Body mass index; CASP, Critical Appraisal Skills Program; GABA, Gamma-aminobutyric acid; GI, gastrointestinal; ESR, erythrocyte sedimentation rate; KEGG, Kyoto Encyclopedia of Genes and Genomes; NT, neurotypical controls; PICRUST, Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; rRNA, ribosomal ribonucleic acid; RETT, Rett’s syndrome; RETT-C, subjects with Rett’s syndrome and constipation; RETT-NC subjects with Rett’s syndrome and without constipation; RETT pre-P, subjects with Rett’s syndrome in their pre-puberty period; RETT post-P, subjects with Rett’s syndrome in their post-puberty period; SCFAs, short chain fatty acids. *Ruminococcaceae renamed to Oscillospiraceae in 2019.