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Table 1 Frequency and semi-quantitative estimation of OTUs within samples and infants

From: Temporal dynamics of the very premature infant gut dominant microbiota

Species-level OTUa(n = 50)

Genus and/or family-level OTUs (n = 19)

Samples with OTU n (%)c

Infants with OTU n (%)d

Period of detection (day)

Semi-quantitative score (band intensity)e

1 (+) n (%) of bands

2 (++) n (%) of bands

3 (+++) n (%) of bands

Staphylococcus epidermidis group*

Staphylococcus

268 (75.7%)

30 (100%)

d3-d53

45 (16.8%)

67 (25%)

156 (58.2%)

Staphylococcus haemolyticus*

Staphylococcus

185 (52.3%)

26 (86.7%)

d4-d51

34 (18.4%)

69 (37.3%)

82 (44.3%)

Staphylococcus warneri*

Staphylococcus

45 (12.7%)

16 (53.3%)

d3-d33

10 (22.2%)

16 (35.6%)

19 (42.2%)

Staphylococcus hominis*

Staphylococcus

13 (13.7%)

6 (20%)

d7-d45

4 (30.8%)

4 (30.8%)

5 (38.4%)

Staphylococcus sp.

Staphylococcus

6 (1.7%)

3 (10%)

d3-d25

2 (33.3%)

3 (50%)

1 (16.7%)

Staphylococcus cohnii

Staphylococcus

4 (1.1%)

1 (3.3%)

d27-d33

4 (100%)

0

0

NDb

Not determined

93 (26.3%)

24 (80%)

d3-d56

60 (64.5%)

16 (17.2%)

17 (18.3%)

Enterococcus faecalis

Enterococcus

98 (27.7%)

18 (60%)

d3-d56

13 (13.3%)

19 (19.4%)

66 (67.3%)

Enterococcus durans group

Enterococcus

7 (2%)

2 (6.7%)

d31-d53

1 (14.3%)

2 (28.6%)

4 (57.1%)

Clostridium butyricum*

Clostridium/Clostridiaceae

40 (11.3%)

12 (40%)

d18-d53

8 (20%)

11 (27.5%)

21 (52.5%)

Clostridium difficile*

Clostridium/Clostridiaceae

34 (9.6%)

11 (36.7%)

d24-d56

14 (41.2%)

17 (50%)

3 (8.8%)

Clostridium neonatale

Clostridium/Clostridiaceae

29 (8.2%)

10 (33.3%)

d16-d53

12 (41.4%)

12 (41.4%)

5 (17.2%)

Clostridium perfringens

Clostridium/Clostridiaceae

23 (6.5%)

9 (30%)

d17-d50

8 (34.8%)

4 (17.4%)

11 (47.8%)

Clostridium sp.

Clostridium/Clostridiaceae

9 (2.5%)

4 (13.3%)

d27-d42

6 (66.7%)

1 (11.1%)

2 (22.2%)

Clostridium paraputrificum

Clostridium/Clostridiaceae

5 (1.4%)

3 (10%)

d15-d18

2 (40%)

2 (40%)

1 (20%)

Clostridium tertium

Clostridium/Clostridiaceae

9 (2.5%)

3 (10%)

d22-d49

3 (33.3%)

3 (33.3%)

3 (33.3%)

Clostridium disporicum group

Clostridium/Clostridiaceae

5 (1.4%)

2 (6.7%)

d15-d24

2 (40%)

2 (40%)

1 (20%)

Clostridium corinoforum

Clostridium/Clostridiaceae

1 (0.3%)

1 (3.3%)

d34

1 (100%)

0

0

Clostridium glycolicum*

Clostridium/Clostridiaceae

1 (0.3%)

1 (3.3%)

d50

1 (100%)

0

0

Clostridium favososporum

Clostridium/Clostridiaceae

5 (1.4%)

1 (3.3%)

d31-d50

3 (60%)

1 (20%)

1 (20%)

Clostridium symbosium group

Clostridium/Clostridiaceae

2 (0.6%)

1 (3.3%)

d21-d27

0

1 (50%)

1 (50%)

Sarcina ventriculi

Sarcina/Clostridiaceae

1 (0.3%)

1 (3.3%)

d17

0

0

1 (100%)

Escherichia coli*

Enterobacteriaceae

22 (6.2%)

8 (26.7%)

d6-d56

11 (50%)

0

11 (50%)

Klebsiella oxytoca

Enterobacteriaceae

13 (3.7%)

4 (13.3%)

d12-d56

4 (30.8%)

1 (7.7%)

8 (61.5%)

Klebsiella pneumoniae

Enterobacteriaceae

3 (0.8%)

2 (6.7%)

d39-d49

0

0

3 (100%)

Enterobacter cloacae

Enterobacteriaceae

5 (1.4%)

1 (3.3%)

d38-d56

1 (20%)

0

4 (80%)

Veillonella dispar

Veillonella

31 (8.8%)

6 (20%)

d4-d56

20 (64.5%)

3 (9.7%)

8 (25.8%)

Veillonella parvula

Veillonella

9 (2.5%)

3 (10%)

d28-d45

1 (11.1%)

5 (55.6%)

3 (33.3%)

Veillonella sp.

Veillonella

7 (2%)

2 (6.7%)

d19-d42

2 (28.6%)

2 (28.6%)

3 (42.8%)

Rothia mucilaginosa

Rothia

10 (2.8%)

4 (13.3%)

d37-d52

3 (30%)

3 (30%)

4 (40%)

Aquabacterium commune*

Aquabacterium/Burkholderiales

7 (2%)

4 (13.3%)

d3-d41

5 (71.4%)

2 (28.6%)

0

Aquabacterium citratiphilum*

Aquabacterium/Burkholderiales

2 (0.6%)

1 (3.3%)

28-d30

1 (50%)

1 (50%)

0

Burkholderiales ND

Burkholderiales

7 (2%)

1 (3.3%)

d16-d33

5 (71.4%)

1 (14.3%)

1 (14.3%)

Streptococcus oralis group

Streptococcus

4 (1.1%)

3 (10%)

d24-d50

2 (50%)

1 (25%)

1 (25%)

Streptococcus salivarius

Streptococcus

10 (2.8%)

2 (6.7%)

d31-d56

5 (50%)

5 (50%)

0

Streptococcus anginosus

Streptococcus

1 (0.3%)

1 (3.3%)

d3

0

0

1 (100%)

Streptococcus oralis/parasanguinis

Streptococcus

1 (0.3%)

1 (3.3%)

d49

1 (100%)

0

0

Streptococcus parasanguinis group

Streptococcus

1 (0.3%)

1 (3.3%)

d42

0

1 (100%)

0

Streptococcus sanguinis group

Streptococcus

1 (0.3%)

1 (3.3%)

d28

1 (100%)

0

0

Streptococcus thermophilus

Streptococcus

5 (1.4%)

1 (3.3%)

d16-d28

2 (40%)

1 (20%)

2 (40%)

Bacillus cereus group

Bacillus/Bacillaceae

4 (1.1%)

4 (13.3%)

d9-d56

3 (75%)

0

1 (25%)

Oceanobacillus sp.

Oceanobacillus/Bacillaceae

3 (0.8%)

1 (3.3%)

d18-d24

3 (100%)

0

0

Bifidobacterium breve*

Bifidobacterium

9 (2.5%)

2 (6.7%)

d3-d49

3 (33.3%)

6 (66.7%)

0

Bifidobacterium longum

Bifidobacterium

5 (1.4%)

2 (6.7%)

d22-d50

3 (60%)

2 (40%)

0

Clostridium innocuum

Erysipelotrichaceae

9 (2.5%)

1 (3.3%)

d10-d36

3 (33.3%)

6 (66.7%)

0

Propionibacterium sp.

Propionibacterium

3 (0.8%)

1 (3.3%)

d18-d24

1 (33.3%)

0

2 (66.7%)

Propionibacterium acnes

Propionibacterium

2 (0.6%)

1 (3.3%)

d43-d45

0

2 (100%)

0

Sneathia sanguinegens

Sneathia

2 (0.6%)

1 (3.3%)

d3-d4

1 (50%)

0

1 (50%)

Pseudomonas sp.

Pseudomonas

1 (0.3%)

1 (3.3%)

d37

0

1 (100%)

0

Anaerococcus octavius

Anaerococcus

2 (0.6%)

1 (3.3%)

d32-d37

0

2 (100%)

0

Corynebacterium tuberculostearicum

Corynebacterium

2 (0.6%)

1 (3.3%)

d14-d15

0

2 (100%)

0

  1. aOTUs are indicated by main groups of decreasing occurence among the 30 preterm infants.
  2. bND, OTU not determined (not included in the total SLOTU number of 50): the group included bands with 37 distinct migration distances.
  3. cNumber and % of samples with OTU among the 354 samples, bold type indicates the species-level OTU mostly represented in samples within the corresponding genus and/or family-level OTU.
  4. dNumber and % of preterm infants with OTU among the 30 neonates, bold type indicates the species-level OTU mostly represented in neonates within the corresponding genus and/or family-level OTU.
  5. eBold type indicates the most frequent semi-quantitative score observed for the OTU within PCR-TTGE patterns.
  6. *OTU identified in patient ZA with NEC.