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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.
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