Table 2

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

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]


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).

Di Cagno et al. BMC Microbiology 2011 11:219   doi:10.1186/1471-2180-11-219

Open Data