TABLE 2.
Tentative identities (16S rRNA gene similarities) and frequencies of isolates randomly picked from colonies appearing on RFGC, MRS, or Rogosa agar after incubation of rectal samples from piglets fed control diets
| Best 16S rRNA gene GenBank matcha (species or clone) | Corresponding porcine cloneb | T-RFc (bp) | Frequency (%) on indicated medium
|
|||
|---|---|---|---|---|---|---|
| Expt 1d
|
Expt 2e
|
|||||
| RFGC | MRS | MRS | Rogosa | |||
| Lactobacillus amylovorus (AY944408) | OTU171 | 596 | 42 | 62 | 53 | |
| Lactobacillus reuteri (X76328) | OTU173 | 406 | 3 | 22 | 14 | 31 |
| Streptococcus alactolyticus (AJ201899) | OTU180 | 581 | 17 | 29 | 10 | |
| Lactobacillus ruminis (M58828) | OTU329 | 1,123 | 3 | 9 | 8 | |
| Lactobacillus mucosae (AF126738) | OTU174 | 267 | 2 | 3 | 2 | |
| Megasphaera elsdenii (U95027) | OTU196 | 591 | 7 | |||
| Mitsuokella multiacida (X81878) | OTU191 | 390 | 7 | |||
| Catenibacterium mitsuokai (AB030221) | OTU376 | 211 | 6 | |||
| Mitsuokella jalaludinii (AF479674) | OTU191 | 390 | 6 | |||
| Mitsuokella multiacida (X81878) | OTU191 | 390 | 5 | |||
| Enterococcus gallinarum (AJ301833) | OTU328 | 218 | 3 | |||
| Lactobacillus vitulinus (M23727) | OTU046 | 75 | 3 | |||
| Roseburia intestinalis (AJ312385) | OTU048 | 190 | 3 | |||
| Staphylococcus epidermis (AY030340) | OTU181 | 238 | 3 | |||
| Staphylococcus hominis (L37601) | OTU181 | 239 | 3 | |||
| Bifidobacterium boum (D86190) | OTU325 | 181 | 2 | |||
| Clostridium celerecrescens (AJ295659) | OTU75 | 190 | 2 | |||
| Enterococcus hirae (AJ420799) | OTU178 | 217 | 1 | 1 | ||
| Eubacterium formicigenerans (L34619) | OTU89 | 1,091 | 2 | |||
| Lactobacillus acidophilus johnsonii (AJ002575) | OTU170 | 1,131 | 2 | |||
| mpn-isolate group 2 (AY028442) | OTU022 | 102 | 2 | |||
| Prevotella bryantii (AJ006457) | OTU016 | 102 | 2 | |||
| Ruminococcus obeum (X85101) | OTU83 | 189 | 2 | |||
| Ruminococcus torques (L76604) | OTU88 | 1,089 | 2 | |||
| UB adh43 (AF132272)f | OTU16 | 104 | 2 | |||
| UB HuCB5 (AJ408989)f | OTU184 | 37 | 2 | |||
| URB 4C3d-9 (AB034082)f | OTU265 | 582 | 2 | |||
| Faecalibacterium prausnitzii (AJ413954) | OTU107 | 37 | 1 | |||
| Lactobacillus delbreuckii (AY050172) | OTU172 | 222 | 1 | |||
| Staphylococcus warneri (L37603) | OTU181 | 237 | 1 | |||
| Uncultured bacterium clonesg | 17 | |||||
The bacterial species and clones are listed together with their GenBank accession numbers. The 16S rRNA gene similarities between isolates and the listed species/clones were higher than 97% unless otherwise stated. Hence, the use of bold characters indicates that the best GenBank match showed <97% similarity.
Operational taxonomic units (GenBank accession numbers AF371468 to AF371949) from the porcine bacterium clone library of Leser et al. (36).
Length of 16S rRNA gene terminal restriction fragments after in silico digestion of GenBank sequences with HhaI, using E. coli position 8 as the 5′ primer start.
Frequencies are based on 100 and 98 colonies picked from rumen agar tubes and MRS agar plates, respectively.
Frequencies are based on 58 and 62 colonies picked from MRS and Rogosa agar plates, respectively.
UB, uncultured bacterium; URB, uncultured rumen bacterium.
Single isolates matching (>97% similarity) different uncultured bacterial clones.