Table 4.
Bacterial operational taxonomic units (OTUs) derived from clone libraries
| Bacterial species* | n† | % |
| Gram negative aerobic bacteria | ||
| Alcaligenes sp | 1 | 0.1 |
| Gram negative anaerobic bacteria | ||
| Veillonella dispar | 1 | 0.1 |
| Veillonella sp oral clone X042 | 1 | 0.1 |
| Fusobacterium nucleatum subsp nucleatum | 3 | 0.3 |
| Dialister sp oral clone BS095 | 4 | 0.4 |
| Dialister pneumosintes | 5 | 0.5 |
| Fusobacterium sp (different clones) | 8 | 0.8 |
| Veillonella atypical | 20 | 2 |
| Gram negative facultative anaerobic bacteria | ||
| Enterobacter aerogenes | 1 | 0.1 |
| Morganella morganii | 1 | 0.1 |
| Salmonella typhi | 1 | 0.1 |
| Serratia marcescens | 1 | 0.1 |
| Shigella flexneri | 1 | 0.1 |
| Shigella sonnei | 2 | 0.2 |
| Klebsiella sp HL1 | 3 | 0.3 |
| Pantoea sp | 3 | 0.3 |
| Klebsiella pneumoniae | 4 | 0.4 |
| Enterobacter cancerogenus LMG 1693 | 10 | 1 |
| Escherichia coli | 90 | 8.8 |
| Gram positive anaerobic bacteria | ||
| Actinomyces sp oral clone CT068 | 1 | 0.1 |
| Clostridium irregularis | 1 | 0.1 |
| Eubacterium halii | 1 | 0.1 |
| Lactobacillus acidophilus johnsonii | 1 | 0.1 |
| Ruminococcus obeum | 1 | 0.1 |
| Clostridium leptum | 2 | 0.2 |
| Clostridium methoxybenzovorans | 2 | 0.2 |
| Clostridium ramosum | 2 | 0.2 |
| Clostridium symbiosum | 2 | 0.2 |
| Peptostreptococcus productus | 2 | 0.2 |
| Clostridium indolis | 3 | 0.3 |
| Clostridium sp | 6 | 0.6 |
| Clostridium glycolicum | 8 | 0.8 |
| Clostridium orbiscindens | 13 | 1.3 |
| Clostridium nexile | 27 | 2.6 |
| Butyrate producing bacterium L2-6 | 32 | 3.1 |
| Ruminococcus gnavus | 52 | 5.1 |
| Ruminococcus hansenii | 75 | 7.3 |
| Gram positive facultative anaerobic bacteria | ||
| Staphylococcus epidermidis | 1 | 0.1 |
| Gram positive aerotolerant anaerobic bacteria | ||
| Lactococcus lactis subsp cremoris | 1 | 0.1 |
| Streptococcus intermedius | 1 | 0.1 |
| Enterococcus faecium | 1 | 0.1 |
| Lactococcus lactis subsp lactis IL1 | 2 | 0.2 |
| Streptococcus sanguis | 2 | 0.2 |
| Streptococcus anginosus | 8 | 0.8 |
| Streptococcus mitis | 11 | 1.1 |
| Streptococcus salivarius | 12 | 1.2 |
| Streptococcus sp (different clones) | 153 | 15.0 |
| Streptococcus parasanguis | 157 | 15.4 |
| Uncultured bacteria | ||
| Uncultured bacteria (different clones) | 279 | 27.3 |
*Nomenclature according to Bergey’s Manual of Determinative Bacteriology (Holt, 1994).
†Full length 16S rDNA sequences from a total of 1019 clones from three biopsies of patients with ulcerative colitis, Crohn’s disease, and a normal control using all bacteria primer sets. Specific bacteria were identified by NCBI BLAST analysis using search results of at least 97% similarity (NCBI BLAST, http://www.ncbi.nlm.nih.gov/).