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Table 2 Species of the Lactobacillus and Enterococcus genera identified in faecal samples by 16S rRNA and pheS or recA gene sequencing

From: Duodenal and faecal microbiota of celiac children: molecular, phenotype and metabolome characterization

Sample Number of isolates Number of strains identifieda Closest relative and identity (%) Accession Number
Treated celiac disease (T-CD) children
1 3 3-IVb Pediococcus pentosaceus (99%) [GenBank:FJ844959.1]
  1, 7 1-VII, 5-XI Enterococcus faecium (99%) [GenBank:FJ982664.1]
  1 1-XII Enterococcus avium (99%) [GenBank:HQ169120.1]
  1 1-20I Lactobacillus plantarum (99%) [GenBank:HQ441200.1]
  1 1-7I Lactobacillus delbrueckii subsp. bulgaricus (99%) [GenBank:CP002341.1]
2 12 6-IV Pediococcus pentosaceus (99%) [GenBank:FJ844959.1]
3 2, 1, 1 2-XIV, 1-6I, 1-1I Enterococcus faecium (99%) [GenBank:HQ293070.1]
  6 6-XVI Enterococcus faecalis (99%) [GenBank:HQ293064.1]
  1 1-9I Lactobacillus salivarius (99%) [GenBank:GU357500.1]
4 1, 3, 2 1-II, 3-V, 2-VII Enterococcus faecium (99%) [GenBank:HQ293070.1]
  3, 1, 1 3-II, 1-IV, 1-V Enterococcus avium (99%) [GenBank:HQ169120.1]
  1 1-24I Lactobacillus casei (99%) [GenBank:HQ379174.1]
  1 1-11I Lactobacillus plantarum (99%) [GenBank:EF439680.1]
5 5 5-VII Enterococcus faecium (99%) [GenBank:FJ982664.1]
  1, 3 1-6I, 2-XIX Enterococcus sp. (99%) [GenBank:AB470317.1]
  1 1-11I Lactobacillus rhamnosus (99%) [GenBank:HM218396.1]
  1, 1 1-1I, 1-8I Lactobacillus fermentum (99%) [GenBank:HQ379178.1]
6 5 1(5I-11I-7I-12I-2I) Enterococcus avium (99%) [GenBank:HQ169120.1]
  4 3-XXII Enterococcus sp. (99%) [GenBank:AB470317.1]
  1, 1 1-1I, 1-3I Lactobacillus plantarum (99%) [GenBank:EF439680.1]
7 1 1-12I Enterococcus avium (99%) [GenBank:HQ169120.1]
  11 4-XX Streptococcus macedonicus (99%) [GenBank:EU163501.1]
8 1 1-VII Enterococcus faecium (99%) [GenBank:HQ293070.1]
  1 1-14I Enterococcus sp. (99%) [GenBank:AB470317.1]
  4, 3, 1, 1, 1, 1 4-III, 3-IV, 1-6I, 1-12I, 1-14I, 1-15I Lactobacillus salivarius (99%) [GenBank:FJ378897.1]
9 2, 3 1-III,3-IV Enterococcus faecalis (99%) [GenBank:HQ293064.1]
  1, 1, 1, 3, 1 10I, 1-V, 1-VI, 3-VII, 1-2I Enterococcus faecium (99%) [GenBank:HQ293070.1]
Treated celiac disease (T-CD) children
  1 1-14Ib Lactobacillus casei (99%) [GenBank:HQ318715.2]
10 1 1-III Enterococcus faecalis (99%) [GenBank:HQ293064.1]
  1 1-VII Enterococcus durans (99%) [GenBank:HM218637.1]
  1 1-VII Enterococcus faecium (99%) [GenBank:HQ293070.1]
  2 2-VIII Enterococcus sp. (99%) [GenBank:AB470317.1]
  2, 1 2-III, 1-3I Lactobacillus salivarius (99%) [GenBank:FJ378897.1]
  2 V Lactobacillus coryniformis (99%) [GenBank:HQ293050.1]
11 1, 1 1-4I, 1-12I Enterococcus sp. (99%) [GenBank:AB470317.1]
  1 1-8I Pediococcus acidilactici (99%) [GenBank:GU904688.1]
  1 1-11I Enterococcus durans (99%) [GenBank:HM218637.1]
  2, 1, 3, 1, 1 2-I, 1-1I, 1(6I, 5I,7I), 1-3I, 1-2I Enterococcus faecium (99%) [GenBank:U385351.1]
12 10 5-IV Pediococcus acidilactici (99%) [GenBank:GU904688.1]
  1 1-6I Enterococcus sp. (99%) [GenBank:AB470317.1]
13 1 3I Enterococcus sp. (99%) [GenBank:AB470317.1]
  1, 7 1-VII, 3-XVIII Enterococcus faecium (99%) [GenBank:HQ293070.1]
14 8, 2 4-III, 2-IX Enterococcus avium (99%) [GenBank:HQ169120.1]
  1 1-IV Pediococcus acidilactici (99%) [GenBank:GU904688.1]
  2, 1, 1, 2 2-I, 1-22I, 1-III, 2-VI Lactobacillus plantarum (99-100%) [GenBank:HQ441200.1]
15 8, 1 8-IV, 1-2I Pediococcus acidilactici (99%) [GenBank:GU904688.1]
  1 1-8I Enterococcus sp. (99%) [GenBank:AB470317.1]
  1 1-XVIII Enterococcus faecium (99%) [GenBank:HQ293070.1]
  1 1-III Lactobacillus casei (99%) [GenBank:HQ379174.1]
16 2 2-X Enterococcus faecium (99%) [GenBank:AB596997.1]
  2, 8 2-XV, 7-XXI Streptococcus pasteurianus (99%) [GenBank:AB457024.1]
  3 1(13I-14I-5I) Enterococcus sp. (99%) [GenBank:AB470317.1]
17 1 1-VI Enterococcus faecium (99%) [GenBank:AB596997.1]
  8 7-XII Enterococcus avium (99%) [GenBank:HQ169120.1]
  3, 1 2-XIII, 1-13I Enterococcus sp. (99%) [GenBank:AB470317.1]
18 6, 6 3-VI, 2-XVII Enterococcus faecium (99%) [GenBank:AB596997.1]
  1 1-13I Enterococcus sp. (99%) [GenBank:AB470317.1]
  3 3-II Lactobacillus rhamnosus (99%) [GenBank:HM218396.1]
Treated celiac disease (T-CD) children
  1 1-14Ib Lactobacillus casei (99%) [GenBank:HQ318715.2]
19 1 1-VII Enterococcus durans (99%) [GenBank:HM218637.1]
  6 5-III Lactobacillus salivarius (99%) [GenBank:FJ378897.1]
  2 2-III Lactobacillus paracasei (99%) [GenBank:HQ423165.1]
  1, 4, 1 24I, 3-III, 23I Lactobacillus casei (99%) [GenBank:HQ379174.1]
  3 3-V Lactobacillus coryniformis 99%) [GenBank:HQ293050.1]
Heathy children (HC)
20 3 1-III Enterococcus sp. (99%) [GenBank:AB470317.1]
  1, 6 1-2I, 3-VII Enterococcus avium (99%) [GenBank:HQ169120.1]
  2 2-XIII Enterococcus faecalis (99%) [GenBank:HQ228219.1]
  1 1-6I Lactobacillus plantarum (99%) [GenBank:EF439680.1]
21 3, 5 3-VI, 4-VII Enterococcus avium (99%) [GenBank:HQ169120.1]
  2 2-XII Enterococcus sp. (99%) [GenBank:AB470317.1]
  1, 1 1-3I, 1-XI Lactobacillus plantarum (99%) [GenBank:EF439680.1]
22 1, 1 1-III, 1-10I Enterococcus sp. (99%) [GenBank:AB470317.1]
  4 3-VI Enterococcus faecium(99%) [GenBank:DQ305313.1]
  5 5-VI Enterococcus avium (99%) [GenBank:HQ169120.1]
  1 1-9I Enterococcus durans (99%) [GenBank:HM218738.1]
  1 1-XI Lactobacillus plantarum (99%) [GenBank:EF439680.1]
  1 1-11I Lactobacillus mucosae (99%) [GenBank:AB425938.1]
23 3 3-III Enterococcus sp. (99%) [GenBank:AB470317.1]
  4 3-IV Enterococcus durans (99%) [GenBank:HM218637.1]
  2 2-VI Enterococcus faecium(99%) [GenBank:FJ982664.1]
  3, 2 3-VI, 2-VII Enterococcus avium (99%) [GenBank:HQ169120.1]
24 1, 1 1-5I, 1-8I Enterococcus faecalis (99%) [GenBank:HM480367.1]
  1, 1, 1, 1, 1 1-9I, 1-4I, 1-XVI, 1-7I, 1-1I Enterococcus faecium (99%) [GenBank:HQ293070.1]
  1, 1 1-XVI, 1-3I Enterococcus durans (99%) [GenBank:HM218637.1]
  1 1-2I Lactobacillus plantarum (99%) [GenBank:EF439680.1]
25 3, 1, 1, 1 2-III, 1-V, 1-XIV, 1-2I Enterococcus sp. (99%) [GenBank:DQ305313.1]
  1 1-VIII Enterococcus faecium (99%) [GenBank:AB596997.1]
Heathy children (HC)
  1 1-IIIb Lactobacillus casei (99%) [GenBank:HQ379174.1]
  3, 1 3-III, 1-XI Lactobacillus plantarum (99%) [GenBank:EF439680.1]
26 4 3-IX Enterococcus sp. (99%) [GenBank:DQ305313.1]
  2, 1 2-XI, 1-11I Enterococcus faecium (99%) [GenBank:FJ982664.1]
  1 1-7I Lactobacillus plantarum (99%) [GenBank:HQ441200.1]
  1, 2, 1, 1, 1 1-13I, 2-VI, 1-8I, 1-2I, 1-7I Lactobacillus casei (99%) [GenBank:HQ379174.1]
27 2, 1, 1 1(3I-13I), 1-1I, 1-6I Enterococcus sp. (99%) [GenBank:DQ305313.1]
  1, 1, 1, 2 1-5I, 1-2I, 1-7I, 2-XVI Enterococcus faecium (99%) [GenBank:AB596997.1]
  3 2-XV Enterococcus durans (99%) [GenBank:HM209741.1]
  1 1-11I Lactobacillus plantarum (99%) [GenBank:EF439680.1]
28 4, 1 4-VIII, 1-1I Enterococcus faecium (99%) [GenBank:AB596997.1]
  1, 1, 2 1(4I-5I), 2-XIV Enterococcus sp. (99%) [GenBank:AB470317.1]
  3 2-I Lactobacillus plantarum (99%) [GenBank:HQ441200.1]
  3 3-II Lactobacillus rhamnosus (99%) [GenBank:HM218396.1]
  1 1-4I Lactobacillus brevis (99%) [GenBank:HQ293087.1]
29 1, 1, 1 12I, 1(10I-11I), 1-1I Enterococcus sp. (99-100%) [GenBank:AB470317.1]
  5, 1, 1 3-II, 1-IV, 1-V Enterococcus durans (99%) [GenBank:HM218637.1]
30 9, 1 5-XVIII, 1-1I Enterococcus faecium (99%) [GenBank:HQ293070.1]
  1 IV Lactobacillus casei (99%) [GenBank:HQ379174.1]
  1, 1, 2 1-4I, 1-13I, 2-XIII Lactobacillus plantarum (99%) [GenBank:EF439680.1]
31 1 1-1I Enterococcus sp. (99%) [GenBank:AB470317.1]
  1 1-3I Enterococcus faecium (99%) [GenBank:HQ293070.1]
  2, 2, 1, 2, 1, 2 2-V, 2-VII, 1-12I, 2-X, 1-4I, 2-XII Lactobacillus plantarum (99%) [GenBank:HQ441200.1]
  1 1-VIII Lactobacillus pentosus (99%) [GenBank:HM067026.1]
32 11 2-I Enterococcus faecium (99%) [GenBank:B470317.1]
  1, 1, 1 1-III, 1-15I, I-12I Lactobacillus casei (99%) [GenBank:HQ379174.1]
33 6 2-X Enterococcus sp. (99%) [GenBank:AB470317.1]
  3, 1, 1, 2 3-III, 1-VII, 1-VIII, 2-IX Lactobacillus plantarum (99%) [GenBank:HQ441200.1]
Heathy children (HC)
34 1 1-4Ib Enterococcus sp. (99%) [GenBank:AB470317.1]
  1 1-II Lactobacillus rhamnosus (99%) [GenBank:HM218396.1]
  2 1-IV Lactobacillus casei (99%) [GenBank:HQ379174.1]
  6 2-XI Lactobacillus plantarum (99%) [GenBank:HQ441200.1]
  1. aRandomly Amplified Polymorphic DNA-Polymerase Chain Reaction (RAPD-PCR) analysis was carried out to exclude clonal relatedness. bNumber of cluster in Figure 4-5-6 A-B).
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