Table 2. Phylogenetic distribution of bacterial 16S rRNA cDNA sequences retrieved from RNA of [13C]- and [12C]-glucose treatments.
|
Phylogenetic affiliationa |
Relative abundance of sequences (%) |
||||||
|---|---|---|---|---|---|---|---|
| Phylum and classes | Order, sub-order (*) and family |
[13C]-glucose |
[12C]-glucose |
||||
| t0, L | t0, H | t24, L | t24, H | t24, L | t24, H | ||
| Actinobacteria (16.5) | Acidimicrobiales (2.2) | ||||||
| Acidimicrobiaceae | — | 3.3 | 1.2 | — | 1.1 | — | |
| Unclassified Acidimicrobineae | 3.4 | 1.1 | 1.2 | — | 2.2 | — | |
| Actinomycetales (13.3) | |||||||
| Corynebacterineae* (Mycobacteriaceae/Dietziaceae/Nocardiaceae) | 1.1 | 8.7 | 1.2 | 1.1 | 3.3 | 8.1 | |
| Micrococcineae* (Microbacteriaceae/Micrococcaceae) | 3.4 | 7.6 | 3.7 | — | 4.4 | 3.5 | |
| Propionibacterineae (Propionibacteriaceae/Nocardioidaceae) | 8.0 | 2.2 | 3.7 | 3.3 | 8.8 | 7.0 | |
| Coriobacteriales (0.2) | |||||||
| Coriobacteriaceae | — | 1.1 | — | — | — | — | |
| Rubrobacterales (0.8) | |||||||
| Rubrobacteraceae | 1.1 | 2.2 | — | — | 1.1 | — | |
| Bacterioidetes (0.6) | Bacteroidales (0.4) | ||||||
| Porphyromonadaceae | 1.1 | — | — | 1.1 | — | — | |
| Cytophagales (0.2) | |||||||
| Incertae sedis | — | — | — | — | 1.1 | — | |
| Chloroflexi (0.2) | Anaerolineales (0.2) | ||||||
| Anaerolineaceae | — | 1.1 | — | — | — | — | |
| Firmicutes (46.2) | Bacillales (2.1) | ||||||
| Bacillaceae | 1.1 | 1.1 | 4.9 | — | 1.1 | 3.5 | |
| Planococcaceae | 1.1 | — | — | — | — | — | |
| Clostridiales (42.0) | |||||||
| Clostridiaceae 1 | 5.7 | 5.4 | 3.7 | 1.1 | 6.6 | 8.1 | |
| Lachnospiraceae I(C. propionicum) | — | — | 3.7 | 27.8 | 16.5 | 23.3 | |
| Lachnospiraceae II | 4.6 | 4.4 | 8.6 | 3.3 | 4.4 | 2.3 | |
| Lachnospiraceae III (C. lentocellum) | 2.3 | 1.1 | 5.0 | 1.1 | 2.2 | 1.2 | |
| Peptostreptococcaceae | 10.2 | 12.0 | 12.4 | 18.9 | 14.3 | 10.5 | |
| Peptococcaceae | — | 1.1 | — | — | — | — | |
| Ruminococcaceae | 1.1 | — | 4.9 | 8.9 | 3.3 | 5.8 | |
| Veillonellaceae | — | — | — | 4.4 | 3.3 | — | |
| Erysipelotrichales (1.1) | |||||||
| Erysipelotrichaceae | 2.3 | 1.1 | 2.5 | — | — | 1.2 | |
| Lactobacillales (0.8) | |||||||
| Aerococcaceae | 2.3 | — | 1.2 | — | — | — | |
| Carnobacteriaceae | — | — | 1.2 | — | — | — | |
| Fusobacteria (5.5) | Fusobacteriales (5.5) | ||||||
| Fusobacteriaceae | 20.5 | 9.8 | — | — | 1.1 | 1.2 | |
| Planctomycetes (5.5) | Planctomycetales (5.5) | ||||||
| Planctomycetaceae I (Gemmata) | 2.3 | 8.7 | 1.2 | — | 1.1 | — | |
| Planctomycetaceae II (Rhodospirellula) | — | 1.1 | — | — | — | 2.3 | |
| Planctomycetaceae III (Pirellula) | 1.1 | 1.1 | 2.5 | — | — | — | |
| Planctomycetaceae IV (Isospaera/Sangulispaera) | — | 1.1 | 2.5 | — | — | 1.2 | |
| Planctomycetaceae V | 1.1 | 1.1 | 1.2 | — | — | 1.2 | |
| Novel familyb | 1.1 | — | — | — | 1.1 | — | |
| Proteobacteria (19.5) | |||||||
| Alphaproteobacteria (3.2) | Rhizobiales (1.7) | ||||||
| Hyphomicrobiaceae | — | 3.3 | 5.0 | — | — | — | |
| Phyllobacteriaceae | — | — | 2.5 | — | — | — | |
| Rhodobacterales (0.2) | |||||||
| Rhodobacteraceae | — | — | 1.2 | — | — | — | |
| Rhodospirillales (1.4) | |||||||
| Acetobacteraceae | — | 1.1 | 1.2 | — | 1.1 | 1.2 | |
| Rhodospirillaceae | — | 1.1 | 2.5 | — | — | — | |
| Betaproteobacteria (0.8) | Burkholderiales (0.6) | ||||||
| Oxalobacteraceae | — | 3.3 | — | — | — | — | |
| Neisseriales(0.2) | |||||||
| Neisseriaceae | — | — | 1.2 | — | — | — | |
| Deltaproteobacteria (4.2) | Myxococcales (4.2) | ||||||
| Novel familyb | — | — | 1.2 | — | — | — | |
| Novel familyb | — | — | — | — | — | 1.2 | |
| Polyangiaceae | 8.0 | 2.2 | 6.2 | — | 4.4 | 2.3 | |
| Gammaproteobacteria (11.4) | Aeromonadales (9.3) | ||||||
| Aeromonadaceae | 8.0 | 8.7 | — | 27.8 | 7.7 | 2.3 | |
| Enterobacteriales (1.3) | |||||||
| Enterobacteriaceae | — | — | — | 1.1 | 3.3 | 3.5 | |
| Methylococcales (0.8) | |||||||
| Methylococcaceae | — | — | 2.5 | — | 2.2 | — | |
| Spirochaetes (0.8) | Spirochaetales (0.8) | ||||||
| Leptospiraceae | — | — | — | — | 3.3 | 1.2 | |
| Tenericutes (4.5) | Mycoplasmatales (4.5) | ||||||
| Mycoplasmataceae | 8.0 | 4.4 | 9.9 | — | 1.1 | 4.7 | |
| Verrucomicrobia (0.8) | Novel familyb(0.8) | 1.1 | — | — | — | — | 3.5 |
Abbreviations: H, ‘heavy' fraction; L, ‘light' fractions; t0, sampling point at the start of incubation; t24 sampling point after 24 h of incubation.
a
Sequences were assigned to bacterial families by using the RDP Classifier, DOTUR analysis and BLASTn search. The number of sequences retrieved from cDNA of ‘heavy' and ‘light' fractions ranged from 81 to 92 (Supplementary Table S1). The percentage of relative abundances for phyla and orders are shown in parentheses.
b
Considered as a novel family based on gene sequence similarities <87.5%.