Table 2.

Gut microbiota alterations in children at CD onset.

Study	Subjects	Sample and Techniques	Microbiota Alterations	Other Findings
El Mouzan et al. [46]	20 CD children 20 fecal controls 19 mucosal controls		Duodenal samples of CD ↑Pseudomonadota phylum ↑Lactobacillus acidophilus, Neisseria spp. ↑Coprococcus spp. Fecal samples of CD ↑Verucomicrobia spp. ↑Clostridium spp. ↑Escherichia spp. ↑Lachnospiraceae_bacterium_oral ↓Bifidobacterium genus ↓Bacteroides spp.	Fecal samples were more diverse and richer in bacteria compared with mucosal samples Bacillota and Bacteroidota were the most abundant phyla in both fecal and mucosal samples
Zafeiropoulou et al. [47]	20 CD children 45 CD under GFD 57 healthy controls 19 children at risk of CD	Fecal sample 16S rRNA sequencing	Untreated CD ↓Clostridium sensu stricto 1 genus ↓Ruminococcus genus	Microbial dysbiosis was not reported in CD compared to healthy controls Alistipes was correlated with the presence of symptoms of CD
Di Base et al. [50]	21 CD children 16 healthy controls	Fecal samples Duodenal sample 16S rRNA sequencing	Duodenal samples of CD ↑Enterobacteriaceae family ↑Bacteroidetes/Streptococcus spp. Fecal samples of CD ↓ Bacteroides–Prevotella ↓Akkermansia spp. ↓Staphylococcaceae family	Patients with abdominal pain ↑Bacillaceae family ↑Enterobaeriaceae family Patients with diarrhea ↓Clostridium cluster XIVa ↓Akkermansia ↑Bacillaceae ↑Fusobacterium
Schippa et al. [62]	20 CD children, before and after GFD 10 healthy controls	Duodenal sample 16S ribosomal DNA analysis compared with TTGE	In CD patients vs. controls ↑Bacteroides vulgatus ↑Escherichia coli Active CD vs. Inactive CD prevalence B. vulgatus (80% vs. 90%) Clostridium coccoides group (50% vs. 90%) Bifidobacterium spp (20% vs. 40%)	Mean interindividual similarity index: 54.9% ± 14.9% Active CD 55.6% ± 15.7% remission state 21.8% ± 30.16% controls Similarity index between CD children before and after GFD: 63.9% ± 15.8%
Sample et al. [63]	22 CD children, before and after GFD 17 healthy controls	Fecal sample16S ribosomal RNA sequencing	Active CD vs. Controls ↑Haemophilus genera ↑Alistipes genera ↑Bacteroides genera
El Mouzan et al. [51]	40 CD children 39 controls	Fecal samples Duodenal sample metagenomic analysis of microbial DNA	Fecal samples of CD ↓Bacteroides intestinalis ↓Burkholderiales bacterium 1-1-47 Mucosal samples of CD ↓Human_endogenous_retrovirus_K)
El Mouzan et al. [61]	40 CD children 39 controls	Fecal samples Duodenal sample metagenomic analysis of microbial DNA	Fecal samples ↑ Human polyomavirus 2, Enterobacteria phage mEpX1, Enterobacteria phage mEpX2	Mucosal samples—no association with CD
El Mouzan et al. [55]	40 CD children 39 controls	Fecal samples Duodenal sample metagenomic analysis of microbial DNA	Fecal samples of CD ↓Pichiaceae family ↓Pichia kudriavzevii ↑Saccharomycetes family ↑Saccharomyces cerevisiae ↑Tricholomataceae family ↑Mucosal samples of CD ↑ Saccharomycetaceae family ↑Candida spp. ↓Pneumocystis spp. ↓Pneumocystis jirovecii	Fecal fungal communities were more abundant than those observed in mucosal samples
Sanchez et al. [64]	32 active CD on GFD 17 8 healthy controls	Duodenal mucosa sample 16S ribosomal RNA sequencing	Active CD ↑Pseudomonadota phylum ↑Enterobacteriaceae family ↑Klebsiella oxytoca ↑Staphylococcus epidermidis ↑Staphylococcus pasteuri ↓Bacillota phylum ↓Streptococcaceae family	Non-active CD ↑Streptococcus mitis group

TTGE—temporal temperature gradient gel electrophoresis; ↑ increased levels; ↓decreased levels.