Table 1.
Comparison of significantly increased OTUs in control samples (healthy or dysbiotic microbiota only) and in samples of co-cultures (healthy microbiota/C. difficile or dysbiotic microbiota/C. difficile).
| Microbiota type +C. difficile ribotype | Increased in co-culture | Increased in control (microbiota only) |
|---|---|---|
| Healthy + 010 | Enterococcus (Otu00004) | Clostridium_XlVb (Otu00043) |
| Barnesiella (Otu00024) | Coprococcus (Otu00028) | |
| Anaerostipes (Otu00029) | Morganella (Otu00107) | |
| Uncl. from Lachnospiraceae (Otu00118) | Coprococcus (Otu00011) | |
| Clostridium_XlVa (Otu00032) | Uncl. from Lachnospiraceae (Otu00015) | |
| Healthy + 014/020 | Enterococcus (Otu00004) | Clostridium_XlVb (Otu00043) |
| Uncl. from Acidaminococcaceae (Otu00068) | Coprococcus (Otu00011) | |
| Barnesiella (Otu00024) | Coprococcus (Otu00028) | |
| Uncl. from Lachnospiraceae (Otu00118) | Morganella (Otu00107) | |
| Butyricicoccus (Otu00051) | Peptostreptococcus (Otu00035) | |
| Healthy + 027 | Enterococcus (Otu00004) | Clostridium_XlVb (Otu00043) |
| Barnesiella (Otu00024) | Morganella (Otu00107) | |
| Clostridium_XlVa (Otu00032) | Coprococcus (Otu00028) | |
| Bacteroides (Otu00048) | Sutterella (Otu00014) | |
| Peptostreptococcus (Otu00035) | ||
| Dysbiotic + 010 | Sutterella (Otu00014) | Dorea (Otu00017) |
| Clostridium_sensu_stricto (Otu00006) | Escherichia_Shigella (Otu00001) | |
| Bacteroides (Otu00002) | Clostridium_XlVa (Otu00032) | |
| Veillonella (Otu00003) | Uncl. from Lachnospiraceae (Otu00015) | |
| Streptococcus (Otu00012) | Oscillibacter (Otu00081) | |
| Dysbiotic + 014/020 | Bacteroides (Otu00002) | Oscillibacter (Otu00081) |
| Sutterella (Otu00014) | Clostridium_XlVa (Otu00032) | |
| Veillonella (Otu00003) | Uncl. from Ruminococcaceae (Otu00030) | |
| Bacteroides (Otu00007) | Uncl. from Eubacteriaceae (Otu00094) | |
| Parabacteroides (Otu00021) | Flavonifractor (Otu00026) | |
| Dysbiotic + 027 | Veillonella (Otu00003) | Dorea (Otu00017) |
| Sutterella (Otu00014) | Clostridium_XlVa (Otu00032) | |
| Streptococcus (Otu00012) | Oscillibacter (Otu00081) | |
| Clostridium_sensu_stricto (Otu00006) | Uncl. from Lachnospiraceae (Otu00015) | |
| Phascolarctobacterium (Otu00023) | Flavonifractor (Otu00026) | |
Presented OTUs were identified by the LEfSe test (mothur software), which uses linear discriminant analysis (LDA) to find OTUs that significantly differ in abundance between cultures of microbiota only (control) and co-cultures of microbiota and C. difficile. For each comparison only top five OTUs with highest LDA scores are presented. For additional information, see Supplementary Tables S2, S3. Uncl., unclassified.