Table S1.
Bacterial species, probes, and probe sets used in this study
| Species | Strain | Phylum | Class | Probe name | Probe oligonucleotide 5′–3′ | Fluorophore, probe set 1 | Fluorophore, probe set 2 | Fluorophore, probe set 3 |
| B. thetaiotaomicron | VPI 5482 | Bacteroidetes | Bacteroidia | Bthe577 | TAACTGTCCACCTACGCT | Alexa 488 | Rhodamine Red X | Alexa 488 |
| B. cellulosilyticus | WH2 | Bacteroidetes | Bacteroidia | Bcel85 | GGTCGCCATCAACCTATTGCT | Alexa 555 | Alexa 594 | Alexa 555 |
| B. vulgatus | ATCC 8482 | Bacteroidetes | Bacteroidia | Bvul264 | CCATCGAAGACTAGGTGGGCC | Alexa 660 | Alexa 660 | Alexa 488 |
| B. ovatus | ATCC 8483 | Bacteroidetes | Bacteroidia | Bova412 | TACGACCCATAGAGCCTTC | Alexa 555 | Alexa 488 | |
| B. caccae | ATCC 43185 | Bacteroidetes | Bacteroidia | Bcac218 | GCATCCCCATCTCATACCG | Alexa 594 | ||
| B. uniformis | ATCC 8492 | Bacteroidetes | Bacteroidia | Buni81 | GTCGCCATCAAACTTAGCAAGC | Pacific Orange | Alexa 488 | |
| P. distasonis | ATCC 8503 | Bacteroidetes | Bacteroidia | Pdis156 | GCGGTATTAGTCCGACTTTCGC | Rhodamine Red X | ||
| E. rectale | ATCC 33656 | Firmicutes | Clostridia | Erec1259 | GCTCGGCTTCACAGCTTTGCTT | Rhodamine Red X | Alexa 532 | |
| R. torques | ATCC 27756 | Firmicutes | Clostridia | Rtor88 | GCTCAGTCACAATCCTCTTCA | Alexa 647 | Alexa 647 | Alexa 647 |
| C. scindens | ATCC 35704 | Firmicutes | Clostridia | Csci87 | TCAGTCGCAAGGCTCCTCGT | Alexa 660 | ||
| C. spiroforme | DSM 1552 | Firmicutes | Erysipelotrichia | Cspi159 | GCGGTCTTAGCTGCCGTTT | Alexa 532 | ||
| F. prausnitzii | M21/2 | Firmicutes | Clostridia | Fpra197 | CTCAAAGCGGATTGCTCCTTT | Alexa 532 | ||
| R. obeum | ATCC 29174 | Firmicutes | Clostridia | Robe76 | AGACCAAATCTGCCGAAGCTTCA | Alexa 532 | ||
| D. longicatena | DSM 13814 | Firmicutes | Clostridia | Dlon180 | CCATGCGGTACCGTGGTCTT | Alexa 532 | ||
| C. aerofaciens | ATCC 25986 | Actinobacteria | Coriobacteriia | Caer280 | TCAACCCGGCTACCCGTT | Alexa 594 | Alexa 405 | Alexa 405 |
| Most bacteria | Eub338 | GCTGCCTCCCGTAGGAGT | Alexa 514 |
All probe oligonucleotide sequences were designed in this study except for the Eub338 probe for most bacteria (81). Probes were labeled at the 5′ end with the fluorophore indicated. Probe set 1 is shown in Figs. 3B and 6; probe set 2 is shown in Fig. 3D; probe set 3 is shown in Figs. 3 A and C and 5. In cases where a probed taxon was not detected in an image, the taxon name was omitted from the figure legend (e.g., E. rectale in Figs. 3B and 6).