Table 2.
Prevalence of unique TRFLP patterns identified are core representatives of the microbiome of the ileal mucosa, ileal lumen content and colonic mucosa of piglets independent of the development of necrotizing enterocolitis (NEC)
| Phylum | Class | Closest relative | Percentage of samples in which each pattern was identified | |||||
| Ileal mucosa | Ileal content | Colonic mucosa | ||||||
| No NEC n = 11 |
NEC n = 13 |
No NEC n = 9 |
NEC n = 10 |
No NEC n = 11 |
NEC n = 14 | |||
| Chloroflexi | Anaerolineae/Chloroflexi | Uncultured/Chloroflexi | 45.5 | 69.2 | 66.7 | 60.0 | 63.6 | 71.4 |
| Cyanobacteria | Cyanobacteria | Nostoc | 36.4 | 46.2 | 22.2 | 40.0 | 18.2 | 21.4 |
| Firmicutes | Clostridia | Clostridium tyrobutyricum | 36.4 | 46.2 | 22.2 | 50.0 | 18.2 | 21.4 |
| Clostridium algidicarnis | 9.1 | 7.7 | 0.0 | 0.0 | 9.1 | 35.7 | ||
| Proteobacteria | Gammaproteobacteria | Alkanindiges | 72.7 | 76.9 | 88.9 | 60.0 | 72.7 | 71.4 |
| Uncultured/Alkanindiges/Acinetobacter | 0.0 | 0.0 | 11.1 | 0.0 | 36.4 | 21.4 | ||
| Uncultured/Microbulbife | 0.0 | 0.0 | 0.0 | 0.0 | 45.5 | 42.9 | ||
| Neptuniibacter | 18.2 | 46.2 | 11.1 | 20.0 | 27.3 | 57.1 | ||
| Uncultured/Photobacterium/Hyphomicrobium sp. | 27.3 | 53.8 | 11.1 | 20.0 | 27.3 | 64.3 | ||
| Klebsiella/Salmonella/Erwinia | 100.0 | 92.3 | 55.6 | 70.0 | 90.9 | 100.0 | ||
| Serratia | 0.0 | 0.0 | 22.2 | 0.0 | 36.4 | 28.6 | ||
| Uncultured/Methylococcaceae | 9.1 | 23.1 | 11.1 | 20.0 | 54.5 | 64.3 | ||
| Betaproteobacteria | Uncultured/Nitrosomonas/Nitrospira | 90.9 | 92.3 | 88.9 | 100 | 63.6 | 100 | |
| Uncultured/Gallionellaceae/Rhodocyclaceae | 9.1 | 15.4 | 11.1 | 0.0 | 54.5 | 21.4 | ||
n = number of samples. Patterns represented were identified in ≥ 3 piglets within a given location per disease condition.