Table 2.
Inventory of glycoside hydrolases (GHs) identified in the Fibrobacteres genomes, organized by functional category.
| CAZy family | Known activity | pfam domain | Fibrobacteria | Chitinivibrionia | Cellulolytic bacteria (35 genomesa) | Bacterial average across 2038 genomes. | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Fibrobacteraceae | Fibromonadaceae | C. alkali- philus ACht1 | Avg | Prevalence (%) | No. of phylab | |||||||||||
| F. succino-genes S85 | AD_80 | AD_ 111 | SR_ 36 | AD_ 312 | IN01_31 | IN01_221 | IN01_307 | MC_ 77 | Avg | |||||||
| CELLULASES | ||||||||||||||||
| GH5 | Cellulase | PF00150 | 13.0 | 16.7 | 16.7 | 15.2 | 18.8 | 27.5 | 18.0 | 15.2 | 6.3 | 23.3 | 2.37 | 1.46 | 30.9 | 17 |
| GH9 | Endoglucanase | PF00759 | 9.0 | 10.3 | 10.4 | 8.7 | 5.8 | 10.0 | 12.8 | 12.1 | 18.8 | 6.7 | 0.91 | 0.31 | 9.6 | 15 |
| GH44 | Endoglucanase | PF12891 | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | – | – | – | – | – | 0.03 | 0.03 | 2.3 | 7 |
| GH45 | Endoglucanase | PF02015 | 4.0 | 3.9 | 5.2 | 4.4 | 2.9 | 2.5 | 7.7 | 9.1 | – | 3.3 | 0.02 | 0.01 | 0.3 | 3 |
| Subtotals (%) | 27.0 | 32.1 | 33.3 | 29.4 | 29.0 | 40.0 | 38.5 | 36.4 | 25.0 | 33.3 | 3.33 | 1.81 | ||||
| CHITINASES | ||||||||||||||||
| GH18 | Chitinase | PF00704 | 2.0 | 2.6 | 2.1 | 2.2 | 2.9 | 2.5 | 2.6 | 3.0 | 3.1 | 3.3 | 3.12 | 2.16 | 30.0 | 19 |
| GH19 | Chitinase | PF00182 | – | – | – | – | – | – | – | – | 6.3 | – | 0.55 | 0.32 | 9.7 | 10 |
| GH20 | β-hexosaminidase | PF00728 | – | – | – | – | – | – | – | – | – | 3.3 | 1.15 | 0.91 | 23.2 | 17 |
| Subtotals (%) | 2.0 | 2.6 | 2.1 | 2.2 | 2.9 | 2.5 | 2.6 | 3.0 | 9.4 | 6.7 | 4.82 | 3.39 | ||||
| HEMICELLULASES | ||||||||||||||||
| GH8 | Endo-xylanases | PF01270 | 6.0 | 3.9 | 7.3 | 7.6 | 5.8 | 5.0 | 5.1 | 3.0 | 15.6 | 3.3 | 0.81 | 0.56 | 20.1 | 17 |
| GH10 | Endo-1,4-β-Xylanase | PF00331 | 8.0 | 5.1 | 7.3 | 6.5 | 2.9 | 2.5 | 2.6 | 3.0 | 6.3 | – | 1.06 | 0.43 | 12.7 | 14 |
| GH11 | Xylanase | PF00457 | 4.0 | 1.3 | 4.2 | 5.4 | 1.5 | 2.5 | 5.1 | 3.0 | – | – | 0.31 | 0.08 | 4.3 | 11 |
| GH26 | β-mannanase and xylanase | PF02156 | 4.0 | 3.9 | 4.2 | 3.3 | 2.9 | – | – | 3.0 | – | – | 0.98 | 0.16 | 6.9 | 11 |
| GH53 | Endo-1,4-β-xylanase | PF07745 | 2.0 | 1.3 | 1.0 | 2.2 | 1.5 | 2.5 | 2.6 | 3.0 | – | – | 0.55 | 0.22 | 10.6 | 14 |
| Subtotals (%) | 24.0 | 15.4 | 21.0 | 25.0 | 14.5 | 12.5 | 15.4 | 15.2 | 21.9 | 3.3 | 3.72 | 1.45 | ||||
| DEBRANCHING ENZYMES | ||||||||||||||||
| GH16 | Xyloglucanases and xyloglycosyltransferases | PF00722 | 4.0 | 5.1 | 4.2 | 3.3 | 4.4 | 0.0 | 0.0 | 0.0 | 3.1 | 0.0 | 1.72 | 0.78 | 19.7 | 20 |
| GH74 | Endoglucanases and oglucanases | – | 2.0 | 3.9 | 2.1 | 2.2 | 2.9 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.27 | 0.10 | 4.3 | 9 |
| GH51 | α-L-arabinofuranosidase | – | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 0.0 | 2.6 | 3.0 | 0.0 | 0.0 | 0.78 | 0.41 | 15.0 | 14 |
| GH54 | α-L-arabinofuranosidase | PF09206 | 1.0 | 0.0 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.00 | 0.02 | 0.9 | 6 |
| Subtotals (%) | 8.0 | 10.3 | 8.3 | 6.5 | 8.7 | 0.0 | 2.6 | 3.0 | 3.1 | 0.0 | 2.77 | 1.31 | ||||
| OLIGOSACCHARIDE-DEGRADING ENZYMES | ||||||||||||||||
| GH1 | β-glucosidase and other β-linked dimers | PF00232 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.1 | 3.3 | 2.73 | 3.66 | 46.6 | 17 |
| GH2 | β-galactosidases and other β–linked dimers | PF00703 PF02836 PF02837 | 2.0 | 2.6 | 2.1 | 2.2 | 2.9 | 0.0 | 0.0 | 3.0 | 3.1 | 0.0 | 2.88 | 1.92 | 38.2 | 18 |
| GH3 | Mainly β-glucosidases | PF00933 PF01915 | 3.0 | 2.6 | 2.1 | 1.1 | 2.9 | 5.0 | 0.0 | 3.0 | 0.0 | 0.0 | 4.68 | 5.87 | 73.4 | 27 |
| GH43 | Arabinases and xylosidases | PF04616 | 14.0 | 11.5 | 9.4 | 13.0 | 13.0 | 5.0 | 5.1 | 0.0 | 0.0 | 3.3 | 2.82 | 1.30 | 22.2 | 15 |
| GH52 | β-xylosidase | PF03512 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.3 | 0.04 | 0.03 | 1.5 | 5 |
| Subtotals (%) | 19.0 | 16.7 | 13.5 | 16.3 | 18.8 | 10.0 | 5.1 | 6.1 | 6.2 | 10.0 | 13.14 | 12.79 | ||||
| CELLOBIOSE/CHITOBIOSE PHOSPHORYLASE | ||||||||||||||||
| GH84 | Cellobiose/chitobiose phosphorylase | PF06165 PF06205 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.1 | 0.0 | 0.23 | 0.16 | 4.8 | 7 |
| GH94 | Cellobiose/chitobiose phosphorylase | PF06165 PF06205 | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 5.0 | 2.6 | 3.0 | 6.3 | 3.3 | 0.58 | 0.69 | 18.8 | 18 |
| Subtotals (%) | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 5.0 | 2.6 | 3.0 | 9.4 | 3.3 | 0.81 | 0.85 | ||||
| OTHERS | ||||||||||||||||
| GH13 | Unknown | PF02903 | 3.0 | 3.9 | 3.1 | 3.3 | 5.8 | 7.5 | 10.3 | 12.1 | 6.3 | 6.7 | 16.52 | 16.67 | 80.2 | 27 |
| GH23 | Lysozyme type G/peptidoglycan lyase/chitinase | – | 3.0 | 3.9 | 3.1 | 3.3 | 4.4 | 12.5 | 10.3 | 12.1 | 12.5 | 20.0 | 8.01 | 17.21 | 80.7 | 30 |
| GH27 | Unknown | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.44 | 0.09 | 5.1 | 10 | |
| GH30 | Glucosylceramidase | PF02055 | 4.0 | 3.9 | 4.2 | 4.4 | 2.9 | 0.0 | 2.6 | 0.0 | 0.0 | 0.0 | 0.52 | 0.31 | 11.6 | 15 |
| GH57 | α-amylase | PF03065 | 3.0 | 3.9 | 2.1 | 2.2 | 2.9 | 5.0 | 2.6 | 3.0 | 3.1 | 10.0 | 0.70 | 2.43 | 22.8 | 27 |
| GH77 | Amylomaltase or 4-α-glucanotransferase | PF02446 | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 2.5 | 2.6 | 3.0 | 3.1 | 3.3 | 1.47 | 3.20 | 55.0 | 26 |
| GH95 | α-1,2-L-fucosidase/α-L-fucosidase | – | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.35 | 0.22 | 9.8 | 14 |
| GH105 | Unknown | PF07470 | 1.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.77 | 0.31 | 12.2 | 14 |
| GH106 | α-L-rhamnosidase | – | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 3.3 | 0.16 | 0.09 | 4.5 | 8 |
| GH109 | α-N-acetylgalactosaminidase | – | 0.0 | 0.0 | 0.0 | 1.1 | 1.5 | 0.0 | 0.0 | 0.0 | 0.0 | 0.0 | 5.81 | 5.61 | 65.1 | 27 |
| GH116 | Unknown | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 2.5 | 2.6 | 3.0 | 0.0 | 0.0 | 0.04 | 0.21 | 4.7 | 9 | |
| GH127 | β-L-arabinofuranosidase | – | 1.0 | 1.3 | 1.0 | 1.1 | 1.5 | 0.0 | 2.6 | 0.0 | 0.0 | 0.0 | 0.77 | 0.32 | 14.7 | 14 |
| Subtotals (%) | 19.0 | 21.8 | 17.7 | 19.6 | 24.7 | 30.0 | 33.3 | 33.3 | 25.0 | 43.3 | 35.51 | 46.67 | ||||
| Total estimated glycoside hydrolases | 100 | 78 | 96 | 92 | 69 | 40 | 39 | 33 | 32 | 30 | – | – | ||||
| (Glycoside hydrolases with signal peptide (%)) | 71.8 | 64.1 | 72.1 | 76.4 | 48.7 | 35.6 | 46.5 | 40.0 | 31.4 | 28.6 | – | – | ||||
| Total estimated genes | 2871 | 2754 | 3008 | 2855 | 2344 | 3391 | 3347 | 2773 | 2304 | 2321 | 4512c | 3395c | ||||
| (Signal peptide to total genes (%)) | 21.2 | 17.9 | 21.6 | 22.0 | 15.2 | 10.8 | 11.1 | 11.5 | 7.4 | 7.7 | ||||||
| % of genes that are glycoside Hydrolases | 3.5 | 2.8 | 3.2 | 3.2 | 2.9 | 1.2 | 1.2 | 1.2 | 1.4 | 1.3 | 1.2d | 0.9d | ||||
a
Based on Koeck et al. (2014).
b
Of a total of 30 bacterial phylum.
c
Estimated average genes across 35 and 2038 bacterial genomes respectively.
d
Average of 116 GHs to total genes of 35 and 2038 bacterial genomes respectively.