Table 4.

Main findings from the studies analyzing the fecal microbiota.

#	References	Microbiome composition results
1	Collado et al. (13)	Bacteroides, Clostridium, and Staphylococcus spp. were the dominant bacterial groups in CD patients, and their levels were higher than in controls. Dominant bacterial groups in controls were Bifidobacterium and Enterobacteriaceae. Bacteroides-Prevotella, Clostridium histolyticum, and Clostridium coccoides groups sulfate-reducing bacteria (SRB) and Atopobium group were significantly higher in CD patients than in controls.
2	Sanz et al. (15)	The fecal microbiota was more diverse in CD patients than in controls. In celiac children one to six different Lactobacillus groups were present; species other than Lactobacillus species were dominant in comparison with controls. The Lactobacillus casei group was more prevalent in control group than in celiac patients. Bifidobacterium species were significantly higher and diverse in controls than in CD patients. Controls combined both infant- and adult-type Bifidobacterium species, while CD patients mainly showed infant-type species (Bifidobacterium bifidum and Bifidobacterium infantis). Bifidobacterium longum, Bifidobacterium pseudocatenulatum, and Bifidobacterium dentium were higher in controls, while the Bifidobacterium bifidum was prevalent in CD group. Bifidobacterium dentium and Bifidobacterium adolescentis were not detected in any CD samples.
3	Collado et al. (16)	Fecal samples showed higher numbers of bifidobacteria than duodenal samples for every analyzed group of bacteria. Bifidobacterium adolescentis was detected more frequently in non-active CD than in active CD and controls. Bifidobacterium dentium was significantly more prevalent in non-active CD than in controls. The most predominant Bifidobacterium species in fecal samples were Bifidobacterium longum, Bifidobacterium catenulatum, and Bifidobacterium bifidum. Total Bifidobacterium levels were significantly higher in controls than in active and non-active CD patients.
4	Collado et al. (17)	Total bacterial counts were significantly lower in control children than in untreated and treated CD patients. Staphylococcus spp. were less prevalent in controls than in untreated and treated CD patients. E. coli was significantly higher in untreated and treated CD patients than in controls. Bacteroides and Clostridium leptum groups were significantly higher in both untreated and treated CD patients than in controls. Bifidobacterium spp. counts were significantly higher in controls than in untreated and treated CD patients. Lactobacillus spp. counts were significantly different only between treated CD patients and controls.
5	Di Cagno et al. (18)	Bacteroides and Clostridium were higher in treated CD and untreated CD than in controls. The ratio of lactic acid bacteria and Bifidobacterium to Bacteroides and enterobacteria, was lower in treated CD. This ratio was even lower in untreated CD. Lactobacillus brevis, Lactobacillus rossiae, and Lactobacillus pentosus were detected only in treated CD patients and controls. Lactobacillus fermentum, Lactobacillus delbrueckii subsp. bulgaricus, and Lactobacillus gasseri were observed only in several fecal samples of healthy controls. Compared to controls the composition of Bifidobacterium species varied for treated CD, while in untreated CD patients there was more variance of these species.
6	De Palma et al. (20)	Gram-positive bacterial population was more common in active CD patients compared to GFD celiac group. Bifidobacterium population was lower in fecal samples of untreated CD patients than in controls. Ig-A coated Bacteroides-Prevotella were higher in controls than in treated and untreated CD patients. Clostridium histolyticum, Clostridium lituseburense, and Faecalibacterium prausnitzii groups were lower in untreated CD than in controls. E. coli, Staphylococcus, Lactobacillus-Enterococcus, and sulfate-reducing bacteria were similar in all three groups studied.
7	Di Cagno et al. (22)	Bacteroides, Porphyromonas, and Prevotella, staphylococci/micrococci and Enterobacteria were more prevalent in fecal samples of treated CD patients. Salmonella, Shigella and Klebsiella, and Clostridium were not significantly different between the groups. Overall, the total anaerobes were the most prevalent in healthy controls. Enterococcus spp. was the largest group among lactic acid bacteria in both patients' groups. Enterococcus faecium was identified nearly in all fecal samples of both groups; Enterococcus avium, Enterococcus faecalis, Enterococcus durans, and Enterococcus spp. were also found. Streptococcus macedonicus, Streptococcus pasteurianus, Pediococcus acidilactici, and Pediococcus pentosaceus were identified in treated CD patients only. The most abundant species of lactobacilli in both groups of children were: Lactobacillus plantarum, Lactobacillus casei, and Lactobacillus rhamnosus. Lactobacillus salivarius, Lactobacillus coryneformis, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus fermentum, and Lactobacillus paracasei were isolated in treated CD patients only. Lactobacillus brevis, Lactobacillus pentosus, and Lactobacillus mucosae were only found in controls. Enterococcus was largest genus isolated among lactic acid bacteria for both patients' groups.
8	Sánchez et al. (25)	Staphylococcus epidermidis was lower in the control group than in active and non-active CD groups. Staphylococcus haemolyticus was higher in active CD group than in controls. Staphylococcus aureus was lower in active CD children compared to non-active CD and controls. Staphylococcus spp. was more diverse in active CD patients than in all the other patients.
9	Pisarello et al. (28)	Lactobacilli were less abundant in the CD patients on GFD than in control children. The enterobacteria population had a trend to increase in CD group compared to healthy controls. Still, there was no significant differences in total counts of the aerobic and anaerobic among two studied groups.
10	Quagliariello et al. (29)	Lactobacillus spp. was more abundant in controls than in CD patients. Bacteroides fragilis was higher in CD group than in controls. No significant differences were detected in levels of Bacteroides. After the treatment with probiotics, the enterobacteria were higher in the controls compared to CD group. Later, after 3 months of probiotic treatment, the levels of enterobacteria declined in the probiotic group.
11	Di Biase et al. (30)	A statistically significant lower relative abundance was detected for Bacteroides/Prevotella cluster in CD group (10.2%) compared to the control group (15.6%). A statistically significant lower abundance in the cluster Akkermansia was found in CD group (0.7%) compared to control patients (4.2%) and, as for the cluster Staphylococcaceae, in CD group (0.9%) compared to healthy controls (2%). The relative abundances of bacterial clusters of duodenal and fecal microbiota were not statistically significantly correlated.