Table 2.
List of the key species differentiating between healthy and CE microbiomes. The species were selected by intersecting the relevant species list coming from differential abundance (DA), RF, and sPLS-DA analyses. Only the species that were present in at least two out of three of these lists were included in this table, where the last column shows the number of methods that identified them as relevant (see Materials and Methods). Species in bold italic are taxa belonging to the core species list (see Results), while the green and orange colored ones are taxa included in or related to the Dysbiosis Index. Taxonomies ending with “s__” mean that there was the best match in Greengenes, but that best match did not have an assignment at the species level. In contrast, a “__” is used to indicate that classification did not arrive down to the species level because a close match did not exist in the reference database or because multiple equivalent matches were available.
| Species | Methods |
|---|---|
| k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Adlercreutzia;s__ | 3 |
| k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella;s__ | 3 |
| k__Bacteria;p__Actinobacteria;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Slackia;s__ | 3 |
| k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__uniformis | 3 |
| k__Bacteria;p__Firmicutes;c__Bacilli;o__Turicibacterales;f__Turicibacteraceae;g__Turicibacter;s__ | 3 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__[Mogibacteriaceae];g__;s__ | 3 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Clostridiaceae;g__Clostridium;s__hiranonis | 3 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__ | 3 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Blautia;s__producta | 3 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Dorea;s__ | 3 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__;s__ | 3 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Allobaculum;s__ | 3 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Clostridium;s__spiroforme | 3 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Coprobacillus;s__ | 3 |
| k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__;s__ | 2 |
| k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__[Paraprevotellaceae];g__[Prevotella];s__ | 2 |
| k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__ | 2 |
| k__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Prevotellaceae;g__Prevotella;s__copri | 2 |
| k__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus;s__ | 2 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__[Ruminococcus];__ | 2 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__[Ruminococcus];s__ | 2 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Lachnospiraceae;g__Roseburia;s__ | 2 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptococcaceae;g__Peptococcus;s__ | 2 |
| k__Bacteria;p__Firmicutes;c__Clostridia;o__Clostridiales;f__Peptostreptococcaceae;g__;s__ | 2 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium];s__ | 2 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__[Eubacterium];s__biforme | 2 |
| k__Bacteria;p__Firmicutes;c__Erysipelotrichi;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Catenibacterium;s__ | 2 |
| k__Bacteria;p__Fusobacteria;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;__;__ | 2 |
| k__Bacteria;p__Proteobacteria;c__Betaproteobacteria;o__Burkholderiales;f__Alcaligenaceae;g__Sutterella;s__ | 2 |
| k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Aeromonadales;f__Succinivibrionaceae;g__Anaerobiospirillum;s__ | 2 |
| k__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacteriales;f__Enterobacteriaceae;__;__ | 2 |