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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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BMC Microbiology

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